Immuno-oncology applications using next generation sequencing

ABSTRACT

Provided herein are systems and methods for generating an immune-oncology profile from a biological sample. The immune-oncology profile can include the proportion or percentage of immune cells, expression of immune escape genes, and/or mutational burden. The immune-oncology profile may allow the generation of classifiers for making prognostic or diagnostic predictions.

CROSS-REFERENCE

This application is a continuation of U.S. application Ser. No. 16/056,406, filed Aug. 6, 2018, which is a continuation of International Application No. PCT/US2018/042176, filed Jul. 13, 2018, which claims the benefit of U.S. Provisional Patent Application No. 62/532,921, filed Jul. 14, 2017, and U.S. Provisional Patent Application No. 62/658,418, filed Apr. 16, 2018, each of which are incorporated herein by reference in their entireties.

BACKGROUND

Cancer is a complex group of diseases involving abnormal cell growth with the potential to invade or spread to other parts of the body. Millions of new cases of cancer occur globally each year. Understanding the immune and tumor profile may help with diagnosis and treatment.

SUMMARY

In an aspect, disclosed herein are methods for generating an immune-oncology profile using ribonucleic acid (RNA) sequencing data, comprising: (a) obtaining RNA sequencing data from a sample obtained from a subject; (b) evaluating at least a subset of the RNA sequencing data to determine level of gene expression for at least one immune modulatory gene; (c) analyzing at least a subset of the RNA sequencing data to calculate a mutational burden based on a plurality of genes from Table 5; (d) applying a deconvolution algorithm to at least a subset of the RNA sequencing data to identify and quantify one or more cell types that are present in the sample based on a plurality of expression signature genes from Tables 1A-1E; and (e) generating an immune-oncology profile based on the level of gene expression determined in (b), the mutational burden calculated in (c), and the one or more cell types quantified in (d). In some instances, the plurality of expression signature genes comprises at least one gene from each of Tables 1A, 1B, 1C, 1D, and 1E. In some instances, the plurality of expression signature genes comprises at least 10, 20, 30, 40, 50, 60, 70, 80, 90, or 100 genes from Table 2, 3, or 4. In some instances, the immune-oncology profile comprises a predicted response to a therapeutic intervention. In some instances, the predicted response is a positive response or a negative response to the therapeutic intervention. In some instances, the positive response comprises tumor regression, slowing tumor progression, or halt of tumor progression. In some instances, the negative response comprises tumor progression, lack of response to the therapeutic intervention, or a combination thereof. In some instances, the therapeutic intervention comprises an immune-therapy. In some instances, the therapeutic intervention further comprises radiation, chemotherapy, surgery, or a combination thereof. In some instances, the method further comprises providing a recommendation based on the immune-oncology profile. In some instances, the recommendation is to start, stop, change, or continue a therapeutic intervention. In some instances, the method further comprises using the profile to provide a therapeutic intervention to the subject. In some instances, the therapeutic intervention is an active immunotherapy, a passive immunotherapy, or a combination thereof. In some instances, the therapeutic intervention is a cancer vaccine, cytokine therapy, immune cell therapy, antibody therapy, or a combination thereof. In some instances, the antibody therapy comprises introducing tumor-targeting monoclonal antibodies, immune cell activating antibodies, or a combination thereof. In some instances, the immune-oncology profile comprises a predicted level of resistance to one or more therapeutic agents based on one or more cancer gene expression signatures identified in (d). In some instances, in (c), the deconvolution algorithm applies a deconvolution matrix to the RNA sequencing data to quantify the one or more cell types that are present in the sample. In some instances, the deconvolution matrix comprises a plurality of immune cell expression signature genes. In some instances, the deconvolution matrix comprises a plurality of tumor cell expression signature genes. In some instances, the deconvolution matrix comprises a plurality of cell types, each cell type comprising a plurality of expression signature genes, wherein expression counts for each expression signature gene is normalized across the plurality of cell types. In some instances, the deconvolution algorithm identifies and quantifies the one or more cell types that are present in the sample using linear least-squares regression (LLSR), quadratic programming (QP), perturbation model for gene expression deconvolution (PERT), robust linear regression (RLR), microarray microdissection with analysis of differences (MMAD), digital sorting algorithm (DSA), or support vector regression. In some instances, in (c) the mutational burden is calculated across at least 500 genes. In some instances, in (c) the mutational burden is calculated across at least 1000 genes. In some instances, in (c) the mutational burden is calculated across at least 2000 genes. In some instances, in (c) the plurality of genes includes at least 500 genes. In some instances, in (c) the plurality of genes includes at least 1000 genes. In some instances, in (d) the plurality of expression signature genes includes at least 100 cell expression signature genes. In some instances, in (d) the plurality of expression signature genes includes at least 200 cell expression signature genes. In some instances, in (d) the plurality of expression signature genes includes genes having a bimodal expression signature between at least two cell types with no more than a 50% overlap between modes. In some instances, in (d) the deconvolution algorithm requires no more than 200 cell expression signature genes to identify and quantify the one or more cell types with at least 90% accuracy for 100 independent samples. In some instances, in (d) the one or more cell types includes at least one leukocyte cell type, stromal cell type, tumor cell type, or a combination thereof. In some instances, in (d) the one or more cell types comprise at least 10 leukocyte types. In some instances, in (d) the one or more cell types comprise at least 20 leukocyte types. In some instances, in (d) the one or more cell types comprise at least 1 tumor cell type. In some instances, (a) comprises obtaining RNA molecules from the sample and measuring the level of gene expression on the RNA molecules. In some instances, (a) comprises obtaining RNA molecules from the sample and performing reverse transcription polymerase chain reaction on the RNA molecules to generate complementary deoxyribonucleic acid (cDNA) molecules, and sequencing the cDNA molecules. In some instances, the cDNA molecules are tagged with unique molecular identifiers and amplified by polymerase chain reaction prior to sequencing. In some instances, (a) comprises performing next generation RNA sequencing on a cDNA library generated from the sample. In some instances, the at least one immune modulatory molecule is CTLA-4, PD-L1, LAG-3, KIR, TIM-3, CECAM1, VISTA, TIGIT, CD73, or a combination thereof. In some instances, the sample is a tumor biopsy. In some instances, the sample is at least one formalin-fixed paraffin-embedded (FFPE) curl. In some instances, the sample has an RNA integrity number (RIN) of no more than 6.0. In some instances, the sample has an RNA integrity number (RIN) of no more than 2.0. In some instances, the sample comprises RNA molecules at least 200 nucleotides in size that constitute no more than 90% of total RNA in the sample. In some instances, the sample comprises RNA molecules at least 200 nucleotides in size that constitute no more than 60% of total RNA in the sample. In some instances, the sample comprises RNA molecules at least 200 nucleotides in size that constitute no more than 30% of total RNA in the sample. In some instances, the sample is obtained from skin, blood, brain, bladder, bone, bone marrow, breast, colon, stomach, esophagus, ovary, uterus, gallbladder, fallopian tube, testicle, kidney, liver, pancreas, adrenal gland, cervix, endometrium, head or neck, lung, prostate, thymus, thyroid, lymph node, or urinary bladder. In some instances, the subject has cancer. In some instances, the method further comprises presenting the immune-oncology profile as a report with graphical elements representing the level of gene expression determined in (b), the mutational burden calculated in (c), and the one or more cell types identified and quantified in (d). In some instances, the level of gene expression determined in (b) is displayed on the report in combination with a reference expression level. In some instances, the mutational burden calculated in (c) is displayed along a single axis having a range between low and high mutational burden. In some instances, the one or more cell types identified and quantified in (d) are displayed in a pie chart indicating a percentage of each cell type in the sample.

In another aspect, disclosed herein are methods for recommending a therapeutic intervention using ribonucleic acid (RNA) sequencing data, comprising: (a) obtaining RNA sequencing data from a sample obtained from a subject; (b) evaluating at least a subset of the RNA sequencing data to determine level of gene expression for at least one immune modulatory gene; (c) analyzing at least a subset of the RNA sequencing data to calculate a mutational burden based on a plurality of genes from Table 5; (d) applying a deconvolution algorithm to at least a subset of the RNA sequencing data to identify and quantify one or more cell types that are present in the sample based on a plurality of expression signature genes from Tables 1A-1E; (e) generating an immune-oncology profile based on the level of gene expression determined in (b), the mutational burden calculated in (c), and the one or more cell types quantified in (d); and (f) recommending a therapeutic intervention based on the immune-oncology profile.

In another aspect, disclosed herein are methods for predicting a clinical outcome using ribonucleic acid (RNA) sequencing data, comprising: (a) obtaining RNA sequencing data from a sample obtained from a subject; (b) evaluating at least a subset of the RNA sequencing data to determine level of gene expression for at least one immune modulatory gene; (c) analyzing at least a subset of the RNA sequencing data to calculate a mutational burden based on a plurality of genes from Table 5; (d) applying a deconvolution algorithm to at least a subset of the RNA sequencing data to identify and quantify one or more cell types that are present in the sample based on a plurality of expression signature genes from Tables 1A-1E; (e) generating an immune-oncology profile based on the level of gene expression determined in (b), the mutational burden calculated in (c), and the one or more cell types quantified in (d); and (f) making a prediction of a clinical outcome to a therapeutic intervention based on the immune-oncology profile, the prediction having a positive predictive value of at least 90% for at least 100 independent samples.

In another aspect, disclosed herein are methods for providing a therapeutic intervention based on ribonucleic acid (RNA) sequencing data, comprising: (a) obtaining RNA sequencing data from a sample obtained from a subject; (b) evaluating at least a subset of the RNA sequencing data to determine level of gene expression for at least one immune modulatory gene; (c) analyzing at least a subset of the RNA sequencing data to calculate a mutational burden based on a plurality of genes from Table 5; (d) applying a deconvolution algorithm to at least a subset of the RNA sequencing data to identify and quantify one or more cell types that are present in the sample based on a plurality of expression signature genes from Tables 1A-1E; (e) generating an immune-oncology profile based on the level of gene expression determined in (b), the mutational burden calculated in (c), and the one or more cell types quantified in (d); and (f) providing a therapeutic intervention based on the immune-oncology profile.

In another aspect, disclosed herein are systems for generating an immune-oncology profile using ribonucleic acid (RNA) sequencing data, comprising: a database comprising the RNA sequencing data from a sample obtained from a subject; and one or more computer processors that are coupled to the database, wherein the one or more computer processors are individually or collectively programmed to: (a) evaluate at least a subset of the RNA sequencing data to determine level of gene expression for at least one immune modulatory gene; (b) analyze at least a subset of the RNA sequencing data to calculate a mutational burden based on a plurality of genes from Table 5; (c) apply a deconvolution algorithm to at least a subset of the RNA sequencing data to identify and quantify one or more cell types that are present in the sample based on a plurality of expression signature genes from Tables 1A-1E; and (d) generate an immune-oncology profile based on the level of gene expression determined in (a), the mutational burden calculated in (b), and the one or more cell types quantified in (c). In some instances, the plurality of expression signature genes comprises at least one gene from each of Tables 1A, 1B, 1C, 1D, and 1E. In some instances, the plurality of expression signature genes comprises at least 10, 20, 30, 40, 50, 60, 70, 80, 90, or 100 genes from Table 2, 3, or 4. In some instances, the immune-oncology profile comprises a predicted response to a therapeutic intervention. In some instances, the predicted response is a positive response or a negative response to the therapeutic intervention. In some instances, the positive response comprises tumor regression, slowing tumor progression, or halt of tumor progression. In some instances, the negative response comprises tumor progression, lack of response to the therapeutic intervention, or a combination thereof. In some instances, the therapeutic intervention comprises an immune-therapy. In some instances, the therapeutic intervention further comprises radiation, chemotherapy, surgery, or a combination thereof. In some instances, the one or more computer processors are programmed to provide a recommendation based on the immune-oncology profile. In some instances, the recommendation is to start, stop, change, or continue a therapeutic intervention. In some instances, the profile is used to provide a therapeutic intervention to the subject. In some instances, the therapeutic intervention is an active immunotherapy, a passive immunotherapy, or a combination thereof. In some instances, the therapeutic intervention is a cancer vaccine, cytokine therapy, immune cell therapy, antibody therapy, or a combination thereof. In some instances, the antibody therapy comprises introducing tumor-targeting monoclonal antibodies, immune cell activating antibodies, or a combination thereof. In some instances, the immune-oncology profile comprises a predicted level of resistance to one or more therapeutic agents based on one or more cancer gene expression signatures identified in (d). In some instances, in (c), the deconvolution algorithm applies a deconvolution matrix to the RNA sequencing data to quantify the one or more cell types that are present in the sample. In some instances, the deconvolution matrix comprises a plurality of immune cell expression signature genes. In some instances, the deconvolution matrix comprises a plurality of tumor cell expression signature genes. In some instances, the deconvolution matrix comprises a plurality of cell types, each cell type comprising a plurality of expression signature genes, wherein expression counts for each expression signature gene is normalized across the plurality of cell types. In some instances, the deconvolution algorithm identifies and quantifies the one or more cell types that are present in the sample using linear least-squares regression (LLSR), quadratic programming (QP), perturbation model for gene expression deconvolution (PERT), robust linear regression (RLR), microarray microdissection with analysis of differences (MMAD), digital sorting algorithm (DSA), or support vector regression (SVR). In some instances, in (c), the mutational burden is calculated across at least 500 genes. In some instances, in (c), the mutational burden is calculated across at least 1000 genes. In some instances, in (c), the mutational burden is calculated across at least 2000 genes. In some instances, in (c) the plurality of genes includes at least 500 genes. In some instances, in (c) the plurality of genes includes at least 1000 genes. In some instances, in (d) the plurality of expression signature genes includes at least 100 cell expression signature genes. In some instances, in (d) the plurality of expression signature genes includes at least 200 cell expression signature genes. In some instances, in (d) the plurality of expression signature genes includes genes having a bimodal expression signature between at least two cell types with no more than a 50% overlap between modes. In some instances, in (d) the deconvolution algorithm requires no more than 200 cell expression signature genes to identify and quantify the one or more cell types with at least 90% accuracy for at least 100 independent samples. In some instances, in (d) the one or more cell types includes at least one leukocyte cell type, stromal cell type, tumor cell type, or a combination thereof. In some instances, in (d) the one or more cell types comprise at least 10 leukocyte types. In some instances, in (d) the one or more cell types comprise at least 20 leukocyte types. In some instances, in (d) the one or more cell types comprise at least 1 tumor cell type. In some instances, (a) comprises obtaining RNA molecules from the sample and measuring the level of gene expression on the RNA molecules. In some instances, (a) comprises obtaining RNA molecules from the sample and performing reverse transcription polymerase chain reaction on the RNA molecules to generate complementary deoxyribonucleic acid (cDNA) molecules, and sequencing the cDNA molecules. In some instances, the cDNA molecules are tagged with unique molecular identifiers and amplified by polymerase chain reaction prior to sequencing. In some instances, (a) comprises performing next generation RNA sequencing on a cDNA library generated from the sample. In some instances, the at least one immune modulatory molecule is CTLA-4, PD-L1, LAG-3, KIR, TIM-3, CECAM1, VISTA, TIGIT, CD73, or a combination thereof. In some instances, the sample is a tumor biopsy. In some instances, the sample is at least one formalin-fixed paraffin-embedded (FFPE) curl. In some instances, the sample has an RNA integrity number (RIN) of no more than 6.0. In some instances, the sample has an RNA integrity number (RIN) of no more than 2.0. In some instances, the sample comprises RNA molecules at least 200 nucleotides in size that constitute no more than 90% of total RNA in the sample. In some instances, the sample comprises RNA molecules at least 200 nucleotides in size that constitute no more than 60% of total RNA in the sample. In some instances, the sample comprises RNA molecules at least 200 nucleotides in size that constitute no more than 30% of total RNA in the sample. In some instances, the sample is obtained from skin, blood, brain, bladder, bone, bone marrow, breast, colon, stomach, esophagus, ovary, uterus, gallbladder, fallopian tube, testicle, kidney, liver, pancreas, adrenal gland, cervix, endometrium, head or neck, lung, prostate, thymus, thyroid, lymph node, or urinary bladder. In some instances, the subject has cancer. In some instances, the immune-oncology profile is presented as a report with graphical elements representing the level of gene expression determined in (b), the mutational burden calculated in (c), and the one or more cell types quantified in (d). In some instances, the level of gene expression determined in (b) is displayed on the report in combination with a reference expression level. In some instances, the mutational burden calculated in (c) is displayed along a single axis having a range between low and high mutational burden. In some instances, the one or more cell types identified and quantified in (d) are displayed in a pie chart indicating a percentage of each cell type in the sample.

In another aspect, disclosed herein are systems for recommending a therapeutic intervention using ribonucleic acid (RNA) sequencing data, comprising: a database comprising the RNA sequencing data from a sample obtained from a subject; and one or more computer processors that are coupled to the database, wherein the one or more computer processors are individually or collectively programmed to: (a) evaluate at least a subset of the RNA sequencing data to determine level of gene expression for at least one immune modulatory gene; (b) analyze at least a subset of the RNA sequencing data to calculate a mutational burden based on a plurality of genes from Table 5; (c) apply a deconvolution algorithm to at least a subset of the RNA sequencing data to identify and quantify one or more cell types that are present in the sample based on a plurality of expression signature genes from Tables 1A-1E; (d) generate an immune-oncology profile based on the level of gene expression determined in (a), the mutational burden calculated in (b), and the one or more cell types quantified in (c); and (e) recommend a therapeutic intervention based on the immune-oncology profile.

In another aspect, disclosed herein are systems for predicting a clinical outcome using ribonucleic acid (RNA) sequencing data, comprising: a database comprising the RNA sequencing data from a sample obtained from a subject; and one or more computer processors that are coupled to the database, wherein the one or more computer processors are individually or collectively programmed to: (a) evaluate at least a subset of the RNA sequencing data to determine level of gene expression for at least one immune modulatory gene; (b) analyze at least a subset of the RNA sequencing data to calculate a mutational burden based on a plurality of genes from Table 5; (c) apply a deconvolution algorithm to at least a subset of the RNA sequencing data to identify and quantify one or more cell types that are present in the sample based on a plurality of expression signature genes from Tables 1A-1E; (d) generate an immune-oncology profile based on the level of gene expression determined in (a), the mutational burden calculated in (b), and the one or more cell types quantified in (c); and (e) make a prediction of a clinical outcome to a therapeutic intervention based on the immune-oncology profile, the prediction having a positive predictive value of at least 90% for at least 100 independent samples.

In another aspect, disclosed herein are methods of analyzing ribonucleic acid (RNA) sequencing data, the method comprising: (a) obtaining a library comprising a plurality of RNA molecules from a sample of a subject; (b) contacting the library with a bait set configured to enrich for RNA molecules corresponding to target genes, the target genes comprising a plurality of genes selected from Tables 1A-1E and Table 5; (c) performing RNA sequencing on the target genes to generate RNA sequencing data; and (d) analyzing the RNA sequencing data to generate an immune-oncology profile comprising: gene expression for at least one immune modulatory gene, mutational burden, and cell type quantification. In some instances, the immune-oncology profile comprises a predicted response to a therapeutic intervention. In some instances, the predicted response is a positive response or a negative response to the therapeutic intervention. In some instances, the positive response comprises tumor regression, slowing tumor progression, or halt of tumor progression. In some instances, the negative response comprises tumor progression, lack of response to the therapeutic intervention, or a combination thereof. In some instances, the therapeutic intervention comprises an immune-therapy. In some instances, the therapeutic intervention further comprises radiation, chemotherapy, surgery, or a combination thereof. In some instances, the methods further comprise providing a recommendation based on the immune-oncology profile. In some instances, the recommendation is to start, stop, change, or continue a therapeutic intervention. In some instances, the methods further comprise using the profile to provide a therapeutic intervention to the subject. In some instances, the therapeutic intervention is an active immunotherapy, a passive immunotherapy, or a combination thereof. In some instances, the therapeutic intervention is a cancer vaccine, cytokine therapy, immune cell therapy, antibody therapy, or a combination thereof. In some instances, the antibody therapy comprises introducing tumor-targeting monoclonal antibodies, immune cell activating antibodies, or a combination thereof. In some instances, the immune-oncology profile comprises a predicted level of resistance to one or more therapeutic agents based on one or more cancer gene expression signatures identified in (d). In some instances, in (d), a deconvolution algorithm applies a deconvolution matrix to the RNA sequencing data to quantify one or more cell types that are present in the sample. In some instances, the deconvolution matrix comprises a plurality of immune cell expression signature genes. In some instances, the deconvolution matrix comprises a plurality of tumor cell expression signature genes. In some instances, the deconvolution matrix comprises a plurality of cell types, each cell type comprising a plurality of expression signature genes, wherein expression counts each expression signature gene is normalized across the plurality of cell types. In some instances, the deconvolution algorithm identifies and quantifies the one or more cell types that are present in the sample using linear least-squares regression (LLSR), quadratic programming (QP), perturbation model for gene expression deconvolution (PERT), robust linear regression (RLR), microarray microdissection with analysis of differences (MMAD), digital sorting algorithm (DSA), or support vector regression. In some instances, the plurality of expression signature genes includes at least 200 cell expression signature genes. In some instances, the plurality of expression signature genes includes genes having a bimodal expression signature between at least two cell types with no more than a 50% overlap between modes. In some instances, the deconvolution algorithm requires no more than 200 cell expression signature genes to identify and quantify the one or more cell types with at least 90% accuracy for 100 independent samples. In some instances, the one or more cell types include at least one leukocyte cell type, stromal cell type, tumor cell type, or a combination thereof. In some instances, the one or more cell types comprise at least 10 leukocyte types. In some instances, the one or more cell types comprise at least 20 leukocyte types. In some instances, the one or more cell types comprise at least 1 tumor cell type. In some instances, in (d), the mutational burden is calculated across at least 500 genes. In some instances, in (d), the mutational burden is calculated across at least 1000 genes. In some instances, in (d), the mutational burden is calculated across at least 2000 genes. In some instances, in (d) the plurality of genes includes at least 500 genes. In some instances, in (d) the plurality of genes includes at least 1000 genes. In some instances, in (d) the plurality of expression signature genes includes at least 100 cell expression signature genes. In some instances, (c) comprises measuring level of gene expression for the target genes. In some instances, (a) comprises obtaining RNA molecules from the sample and performing reverse transcription polymerase chain reaction on the RNA molecules to generate complementary deoxyribonucleic acid (cDNA) molecules, and sequencing the cDNA molecules. In some instances, the at least one immune modulatory molecule is CTLA-4, PD-L1, LAG-3, KIR, TIM-3, CECAM1, VISTA, TIGIT, CD73, or a combination thereof. In some instances, the sample is a tumor biopsy. In some instances, the sample is at least one formalin-fixed paraffin-embedded (FFPE) curl. In some instances, the sample has an RNA integrity number (RIN) of no more than 6.0. In some instances, the sample has an RNA integrity number (RIN) of no more than 2.0. In some instances, the sample comprises RNA molecules at least 200 nucleotides in size that constitute no more than 90% of total RNA in the sample. In some instances, the sample comprises RNA molecules at least 200 nucleotides in size that constitute no more than 60% of total RNA in the sample. In some instances, the sample comprises RNA molecules at least 200 nucleotides in size that constitute no more than 30% of total RNA in the sample. In some instances, the sample is obtained from skin, blood, brain, bladder, bone, bone marrow, breast, colon, stomach, esophagus, ovary, uterus, gallbladder, fallopian tube, testicle, kidney, liver, pancreas, adrenal gland, cervix, endometrium, head or neck, lung, prostate, thymus, thyroid, lymph node, or urinary bladder. In some instances, the subject has cancer. In some instances, the methods further comprise presenting the immune-oncology profile as a report with graphical elements representing the level of gene expression determined in (b), the mutational burden calculated in (c), and the one or more cell types quantified in (d). In some instances, the level of gene expression determined in (b) is displayed on the report in combination with a reference expression level. In some instances, the mutational burden calculated in (c) is displayed along a single axis having a range between low and high mutational burden. In some instances, the one or more cell types identified and quantified in (d) are displayed in a pie chart indicating a percentage of each cell type in the sample.

In another aspect, disclosed herein are methods of analyzing a data set comprising information from a plurality of components from a single source, the method comprising: (a) obtaining the data set, the data set comprising sequence and quantity information for a plurality of data members across the plurality of components; (b) evaluating at least a subset of the data set to determine a numerical quantifier for at least one data member; (c) analyzing at least a subset of the data set to calculate a variation indicator based on the sequence information; (d) applying a deconvolution algorithm to at least a subset of the data set to identify and quantify one or more components that constitute the plurality of components based on a plurality of data member signatures; and (e) generating an output profile based on the numerical quantifier determined in (b), the variation indicator calculated in (c), and the one or more components identified and quantified in (d). In some instances, the output profile comprises a predicted response to a procedure. In some instances, the predicted response is a positive response or a negative response to the procedure. In some instances, the methods further comprise providing a recommendation based on the output profile. In some instances, the recommendation is to start, stop, change, or continue a procedure. In some instances, the methods further comprise using the profile to provide a procedure. In some instances, in (d), the deconvolution algorithm applies a deconvolution matrix to the subset of the data set to identify and quantify the one or more components that constitute the plurality of components. In some instances, the deconvolution matrix comprises a plurality of data member signatures for a plurality of components. In some instances, the deconvolution matrix comprises a plurality of components, each component comprising a plurality of data member signatures, wherein each data member signature is normalized across the plurality of components. In some instances, the deconvolution algorithm identifies and quantifies the plurality of components using linear least-squares regression (LLSR), quadratic programming (QP), perturbation model for gene expression deconvolution (PERT), robust linear regression (RLR), microarray microdissection with analysis of differences (MMAD), digital sorting algorithm (DSA), or support vector regression. In some instances, in (d), the variation indicator is calculated across at least 500 data members. In some instances, in (d), the variation indicator is calculated across at least 1000 data members. In some instances, in (d), the variation indicator is calculated across at least 2000 data members. In some instances, in (d) the plurality of data members includes at least 500 data members. In some instances, in (d) the plurality of data members includes at least 1000 data members. In some instances, in (d) the plurality of data member signatures includes at least 100 data member signatures. In some instances, the plurality of data member signatures includes at least 200 data member signatures. In some instances, the plurality of data member signatures includes data member signatures having a bimodal expression signature between at least two components with no more than a 50% overlap between modes. In some instances, the deconvolution algorithm requires no more than 200 data member signatures to identify and quantify the one or more components with at least 90% accuracy for 100 independent data sets. In some instances, the methods further comprise presenting the output profile as a report with graphical elements representing the numerical quantifier for at least one data member determined in (b), the variation indicator calculated in (c), and the one or more components identified and quantified in (d). In some instances, numerical quantifier for at least one data member determined in (b) is displayed on the report in combination with a reference numerical quantifier. In some instances, the variation indicator calculated in (c) is displayed along a single axis having a range between low and high variation. In some instances, the one or more components identified and quantified in (d) are displayed in a pie chart indicating a percentage of each component.

In another aspect, disclosed herein are methods of making a recommendation based on a data set comprising information from a plurality of components from a single source, the method comprising: (a) obtaining the data set, the data set comprising sequence and quantity information for a plurality of data members across the plurality of components; (b) evaluating at least a subset of the data set to determine a numerical quantifier for at least one data member; (c) analyzing at least a subset of the data set to calculate a variation indicator based on the sequence information; (d) applying a deconvolution algorithm to at least a subset of the data set to identify and quantify one or more components that constitute the plurality of components based on a plurality of data member signatures; (e) generating an output profile based on the numerical quantifier determined in (b), the variation indicator calculated in (c), and the one or more components identified and quantified in (d); and (f) recommending a procedure based on the output profile.

In another aspect, disclosed herein are methods of making a recommendation based on a data set comprising information from a plurality of components from a single source, the method comprising: (a) obtaining the data set, the data set comprising sequence and quantity information for a plurality of data members across the plurality of components; (b) evaluating at least a subset of the data set to determine a numerical quantifier for at least one data member; (c) analyzing at least a subset of the data set to calculate a variation indicator based on the sequence information; (d) applying a deconvolution algorithm to at least a subset of the data set to identify and quantify one or more components that constitute the plurality of components based on a plurality of data member signatures; (e) generating an output profile based on the numerical quantifier determined in (b), the variation indicator calculated in (c), and the one or more components identified and quantified in (d); and (f) making a prediction of an outcome to a procedure based on the output profile, the prediction having a positive predictive value of at least 90% for at least 100 independent data sets.

In another aspect, disclosed herein are systems for analyzing a data set comprising information from a plurality of components from a single source, comprising: a database comprising the data set; and one or more computer processors that are coupled to the database, wherein the one or more computer processors are individually or collectively programmed to: (a) obtain the data set, the data set comprising sequence and quantity information for a plurality of data members across the plurality of components; (b) evaluate at least a subset of the data set to determine a numerical quantifier for at least one data member; (c) analyze at least a subset of the data set to calculate a variation indicator based on the sequence information; (d) apply a deconvolution algorithm to at least a subset of the data set to identify and quantify one or more components that constitute the plurality of components based on a plurality of data member signatures; and (e) generate an output profile based on the numerical quantifier determined in (b), the variation indicator calculated in (c), and the one or more components identified and quantified in (d). In some instances, the output profile comprises a predicted response to a procedure. In some instances, the predicted response is a positive response or a negative response to the procedure. In some instances, the output profile is used to provide a recommendation. In some instances, the recommendation is to start, stop, change, or continue a procedure. In some instances, the output profile is used to provide a procedure. In some instances, in (d), the deconvolution algorithm applies a deconvolution matrix to the subset of the data set to identify and quantify the one or more components that constitute the plurality of components. In some instances, the deconvolution matrix comprises a plurality of data member signatures for a plurality of components. In some instances, the deconvolution matrix comprises a plurality of component signatures, each component signature comprising a plurality of data member signatures, wherein each data member signature is normalized across the plurality of component signatures. In some instances, the deconvolution algorithm identifies and quantifies the plurality of components using linear least-squares regression (LLSR), quadratic programming (QP), perturbation model for gene expression deconvolution (PERT), robust linear regression (RLR), microarray microdissection with analysis of differences (MMAD), digital sorting algorithm (DSA), or support vector regression. In some instances, in (d), the variation indicator is calculated across at least 500 data members. In some instances, in (d), the variation indicator is calculated across at least 1000 data members. In some instances, in (d), the variation indicator is calculated across at least 2000 data members. In some instances, in (d) the plurality of data members includes at least 500 data members. In some instances, in (d) the plurality of data members includes at least 1000 data members. In some instances, in (d) the plurality of data member signatures includes at least 100 data member signatures. In some instances, the plurality of data member signatures includes at least 200 data member signatures. In some instances, the plurality of data member signatures includes data member signatures having a bimodal expression signature between at least two component signatures with no more than a 50% overlap between modes. In some instances, the deconvolution algorithm requires no more than 200 data member signatures to identify and quantify the one or more components with at least 90% accuracy for 100 independent data sets. In some instances, the output profile is presented as a report with graphical elements representing the numerical quantifier for at least one data member determined in (b), the variation indicator calculated in (c), and the one or more components identified and quantified in (d). In some instances, the numerical quantifier for at least one data member determined in (b) is displayed on the report in combination with a reference numerical quantifier. In some instances, the variation indicator calculated in (c) is displayed along a single axis having a range between low and high variation. In some instances, the one or more components identified and quantified in (d) are displayed in a pie chart indicating a percentage of each component.

In another aspect, disclosed herein are systems for analyzing a data set comprising information from a plurality of components from a single source, comprising: a database comprising the data set; and one or more computer processors that are coupled to the database, wherein the one or more computer processors are individually or collectively programmed to: (a) obtain the data set, the data set comprising sequence and quantity information for a plurality of data members across the plurality of components; (b) evaluate at least a subset of the data set to determine a numerical quantifier for at least one data member; (c) analyze at least a subset of the data set to calculate a variation indicator based on the sequence information; (d) apply a deconvolution algorithm to at least a subset of the data set to identify and quantify one or more components that constitute the plurality of components based on a plurality of data member signatures; (e) generate an output profile based on the numerical quantifier determined in (b), the variation indicator calculated in (c), and the one or more components identified and quantified in (d); and (f) recommend a procedure based on the output profile.

In another aspect, disclosed herein are systems for analyzing a data set comprising information from a plurality of components from a single source, comprising: a database comprising the data set; and one or more computer processors that are coupled to the database, wherein the one or more computer processors are individually or collectively programmed to: (a) obtain the data set, the data set comprising sequence and quantity information for a plurality of data members across the plurality of components; (b) evaluate at least a subset of the data set to determine a numerical quantifier for at least one data member; (c) analyze at least a subset of the data set to calculate a variation indicator based on the sequence information; (d) apply a deconvolution algorithm to at least a subset of the data set to identify and quantify one or more components that constitute the plurality of components based on a plurality of data member signatures; (e) generate an output profile based on the numerical quantifier determined in (b), the variation indicator calculated in (c), and the one or more components identified and quantified in (d); and (f) make a prediction of an outcome to a procedure based on the output profile, the prediction having a positive predictive value of at least 90% for at least 100 independent data sets.

In another aspect, disclosed herein are methods for generating an immune-oncology profile using ribonucleic acid (RNA) sequencing data, comprising: (a) obtaining RNA sequencing data from a sample obtained from a subject; (b) evaluating at least a subset of the RNA sequencing data to determine level of gene expression for at least one immune modulatory gene; (c) analyzing at least a subset of the RNA sequencing data to calculate a mutational burden based on a plurality of genes, wherein the mutation burden is calculated with a correlation of at least about 80% with a mutational burden Gold Standard; (d) applying a deconvolution algorithm to at least a subset of the RNA sequencing data to identify and quantify one or more cell types that are present in the sample based on a plurality of expression signature genes, wherein the one or more cell types are identified and quantified with a correlation of at least about 80% with a deconvolution Gold Standard; and (e) generating an immune-oncology profile based on the level of gene expression determined in (b), the mutational burden calculated in (c), and the one or more cell types quantified in (d). In some instances, the mutational burden is calculated with a correlation of at least about 90% with the mutational burden Gold Standard. Sometimes, the one or more cell types are identified and quantified with a correlation of at least about 90% with the deconvolution Gold Standard.

In another aspect, disclosed herein are methods for generating an immune-oncology profile using ribonucleic acid (RNA) sequencing data, comprising: (a) obtaining RNA sequencing data from a sample obtained from a subject; (b) evaluating at least a subset of the RNA sequencing data to determine level of gene expression for at least one immune modulatory gene; (c) analyzing at least a subset of the RNA sequencing data to calculate a mutational burden based on a plurality of genes, wherein the mutation burden is calculated at an accuracy of at least about 80%; (d) applying a deconvolution algorithm to at least a subset of the RNA sequencing data to identify and quantify one or more cell types that are present in the sample based on a plurality of expression signature genes, wherein the one or more cell types are identified and quantified at an accuracy of at least about 80%; and (e) generating an immune-oncology profile based on the level of gene expression determined in (b), the mutational burden calculated in (c), and the one or more cell types quantified in (d). In some instances, the mutational burden is calculated at a specificity of at least about 90%. Sometimes, the one or more cell types are identified and quantified at a specificity of at least about 90%.

In another aspect, disclosed herein are methods for generating an immune-oncology profile using ribonucleic acid (RNA) sequencing data, comprising: (a) obtaining RNA sequencing data from a sample obtained from a subject; (b) evaluating at least a subset of the RNA sequencing data to determine level of gene expression for at least one immune modulatory gene; (c) analyzing at least a subset of the RNA sequencing data to calculate a mutational burden based on a plurality of genes, wherein the mutation burden is calculated at a specificity of at least about 80%; (d) applying a deconvolution algorithm to at least a subset of the RNA sequencing data to identify and quantify one or more cell types that are present in the sample based on a plurality of expression signature genes, wherein the one or more cell types are identified and quantified at a specificity of at least about 80%; and (e) generating an immune-oncology profile based on the level of gene expression determined in (b), the mutational burden calculated in (c), and the one or more cell types quantified in (d). In some cases, the mutational burden is calculated at a specificity of at least about 90%. Sometimes, the one or more cell types are identified and quantified at a specificity of at least about 90%.

In another aspect, disclosed herein are methods for generating an immune-oncology profile using ribonucleic acid (RNA) sequencing data, comprising: (a) obtaining RNA sequencing data from a sample obtained from a subject; (b) evaluating at least a subset of the RNA sequencing data to determine level of gene expression for at least one immune modulatory gene; (c) analyzing at least a subset of the RNA sequencing data to calculate a mutational burden based on a plurality of genes, wherein the mutation burden is calculated at a sensitivity of at least about 80%; (d) applying a deconvolution algorithm to at least a subset of the RNA sequencing data to identify and quantify one or more cell types that are present in the sample based on a plurality of expression signature genes, wherein the one or more cell types are identified and quantified at a sensitivity of at least about 80%; and (e) generating an immune-oncology profile based on the level of gene expression determined in (b), the mutational burden calculated in (c), and the one or more cell types quantified in (d). Sometimes, the mutational burden is calculated at a sensitivity of at least about 90%. In certain instances, the one or more cell types are identified and quantified at a sensitivity of at least about 90%.

In another aspect, disclosed herein are methods for identifying at least one cell type in a biological sample comprising a plurality of cell types, comprising: (a) obtaining the biological sample from a subject and enriching for ribonucleic acids (RNA) corresponding to a plurality of expression signature genes present in a deconvolution matrix, the deconvolution matrix tailored to identify cell types present in the biological sample based on sample type; (b) sequencing the RNA to obtain RNA sequencing data; (c) determining a level of gene expression for the RNA enriched from the biological sample; (d) applying the deconvolution matrix to evaluate at least a subset of the RNA sequencing data and the level of gene expression to identify a plurality of cell types and proportions of the plurality of cell types at an accuracy of at least 90%. In some instances, the plurality of cell types includes at least two cell types. Sometimes, the plurality of cell types includes at least three cell types. In various aspects, the biological sample is a non-cancer sample. In certain cases, the biological sample is a cancer sample. The biological sample is oftentimes a non-cancer sample. In some instances, the plurality of expression signature genes comprises at least one gene from at least two of Tables 1A, 1B, 1C, 1D, and 1E. Sometimes, the plurality of expression signature genes comprises at least one gene from at least three of Tables 1A, 1B, 1C, 1D, and 1E. In various aspects, the plurality of expression signature genes comprises at least one gene from at least four of Tables 1A, 1B, 1C, 1D, and 1E. In certain cases, the plurality of expression signature genes comprises at least one gene from each of Tables 1A, 1B, 1C, 1D, and 1E. In some instances, the plurality of expression signature genes comprises at least 10, 20, 30, 40, 50, 60, 70, 80, 90, or 100 genes from Table 2, 3, or 4. Oftentimes, the method further comprises predicting a disease diagnosis based on the plurality of cell types and proportions of the plurality of cell types. In certain instances, sequencing the RNA comprises performing reverse transcription on the RNA to generate complementary DNA (cDNA). Sometimes, the method further comprises sequencing the cDNA or a derivative thereof to obtain the RNA sequencing data.

In some aspects, disclosed herein are methods for identifying at least one cell type in a biological sample comprising a plurality of cell types, comprising: (a) obtaining the biological sample from a subject and enriching for ribonucleic acids (RNA) corresponding to a plurality of expression signature genes present in a deconvolution matrix, the deconvolution matrix tailored to identify cell types present in the biological sample based on sample type; (b) sequencing the RNA to obtain RNA sequencing data; (c) determining a level of gene expression for the RNA enriched from the biological sample; (d) applying the deconvolution matrix to evaluate at least a subset of the RNA sequencing data and the level of gene expression to identify a plurality of cell types and proportions of the plurality of cell types at a specificity of at least 90%. In some instances, the plurality of cell types includes at least two cell types. Sometimes, the plurality of cell types includes at least three cell types. In various aspects, the biological sample is a non-cancer sample. In certain cases, the biological sample is a cancer sample. The biological sample is oftentimes a non-cancer sample. In some instances, the plurality of expression signature genes comprises at least one gene from at least two of Tables 1A, 1B, 1C, 1D, and 1E. Sometimes, the plurality of expression signature genes comprises at least one gene from at least three of Tables 1A, 1B, 1C, 1D, and 1E. In various aspects, the plurality of expression signature genes comprises at least one gene from at least four of Tables 1A, 1B, 1C, 1D, and 1E. In certain cases, the plurality of expression signature genes comprises at least one gene from each of Tables 1A, 1B, 1C, 1D, and 1E. In some instances, the plurality of expression signature genes comprises at least 10, 20, 30, 40, 50, 60, 70, 80, 90, or 100 genes from Table 2, 3, or 4. Oftentimes, the method further comprises predicting a disease diagnosis based on the plurality of cell types and proportions of the plurality of cell types. In certain instances, sequencing the RNA comprises performing reverse transcription on the RNA to generate complementary DNA (cDNA). Sometimes, the method further comprises sequencing the cDNA or a derivative thereof to obtain the RNA sequencing data.

In another aspect, disclosed herein are methods for identifying at least one cell type in a biological sample comprising a plurality of cell types, comprising: (a) obtaining the biological sample from a subject and enriching for ribonucleic acids (RNA) corresponding to a plurality of expression signature genes present in a deconvolution matrix, the deconvolution matrix tailored to identify cell types present in the biological sample based on sample type; (b) sequencing the RNA to obtain RNA sequencing data; (c) determining a level of gene expression for the RNA enriched from the biological sample; (d) applying the deconvolution matrix to evaluate at least a subset of the RNA sequencing data and the level of gene expression to identify a plurality of cell types and proportions of the plurality of cell types at a sensitivity of at least 90%. In some instances, the plurality of cell types includes at least two cell types. Sometimes, the plurality of cell types includes at least three cell types. In various aspects, the biological sample is a non-cancer sample. In certain cases, the biological sample is a cancer sample. The biological sample is oftentimes a non-cancer sample. In some instances, the plurality of expression signature genes comprises at least one gene from at least two of Tables 1A, 1B, 1C, 1D, and 1E. Sometimes, the plurality of expression signature genes comprises at least one gene from at least three of Tables 1A, 1B, 1C, 1D, and 1E. In various aspects, the plurality of expression signature genes comprises at least one gene from at least four of Tables 1A, 1B, 1C, 1D, and 1E. In certain cases, the plurality of expression signature genes comprises at least one gene from each of Tables 1A, 1B, 1C, 1D, and 1E. In some instances, the plurality of expression signature genes comprises at least 10, 20, 30, 40, 50, 60, 70, 80, 90, or 100 genes from Table 2, 3, or 4. Oftentimes, the method further comprises predicting a disease diagnosis based on the plurality of cell types and proportions of the plurality of cell types. In certain instances, sequencing the RNA comprises performing reverse transcription on the RNA to generate complementary DNA (cDNA). Sometimes, the method further comprises sequencing the cDNA or a derivative thereof to obtain the RNA sequencing data.

The present disclosure also provides computer-implemented methods for analyzing a biological sample obtained from a subject having a disease or condition, comprising: (a) obtaining gene expression data comprising the expression of at least one immune modulatory gene from the biological sample; (b) identifying and quantifying a percentage of at least one cell type that is present in the biological sample based on a plurality of expression signature genes; and (c) using a classifier to analyze the expression of the at least one immune modulatory gene and the percentage of the at least one cell type in order to classify the sample. In some instances, the sample is classified into one of at least two groups. In some instances, the at least two groups comprise a group having a positive response to a therapeutic intervention to the disease or condition and a group having a negative response to the therapeutic intervention. In some instances, the positive response comprises tumor regression, slowing tumor progression, or halt of tumor progression. In some instances, the negative response comprises tumor progression, lack of response to the therapeutic intervention, or a combination thereof. In some instances, the therapeutic intervention comprises immunotherapy. In some instances, the immunotherapy comprises a cancer vaccine, cytokine therapy, immune cell therapy, antibody therapy, or any combination thereof. In some instances, the therapeutic intervention comprises radiation, chemotherapy, surgery, or a combination thereof. In some instances, the method further comprises providing instructions to start, stop, change, or continue the therapeutic intervention. In some instances, the disease or condition is cancer. In some instances, the at least one cell type comprises at least one immune cell type. In some instances, the at least one immune cell type is selected from the group consisting of CD4+ memory T-cells, CD4+ naive T-cells, CD4+ T-cells, central memory T (Tcm) cells, effector memory T (Tem) cells, CD4+ Tcm, CD4+ Tem, CD8+ T-cells, CD8+ naive T-cells, CD8+ Tcm, CD8+ Tem, regulatory T cells (Tregs), T helper (Th) 1 cells, Th2 cells, gamma delta T (Tgd) cells, natural killer (NK) cells, natural killer T (NKT) cells, B-cells, naive B-cells, memory B-cells, class-switched memory B-cells, pro B-cells, and plasma cells. In some instances, the at least one immune cell type is selected from the group consisting of M1 macrophages, M2 macrophages, CD19+ B cells, CD14+ monocytes, CD56+ NK cells, CD8+ T cells, Treg cells, and CD4+ T cells. In some instances, the at least one immune modulatory gene is selected from the group consisting of CTLA4, OX40, PD-1, IDO1, CD47, PD-L1, TIM-3, BTLA, ICOS, and ARG1. In some instances, the at least one cell type comprises at least 2, 3, 4, 5, 6, 7, or 8 cell types. In some instances, the at least immune modulatory gene comprises at least 2, 3, 4, 5, 6, 7, 8, 9, or 10 genes. In some instances, the classifier is generated using a machine learning algorithm. In some instances, the machine learning algorithm is a random forest algorithm. In some instances, the classifier is trained using data from no more than 50 samples. In some instances, the biological sample comprises cancer or pre-cancer tissue. In some instances, the prediction of an outcome for the subject is a positive response or a negative response to a therapeutic intervention. In some instances, the prediction of an outcome for the subject is a prognosis of the disease or condition. In some instances, the percentage of the at least one cell type is generated using a deconvolution algorithm that applies a deconvolution matrix to RNA sequencing data for the biological sample. In some instances, the deconvolution algorithm applies a deconvolution matrix to the gene expression data to identify and quantify the percentage of the at least one cell type. In some instances, the deconvolution matrix comprises a plurality of immune cell expression signature genes. In some instances, the deconvolution matrix comprises a plurality of tumor cell expression signature genes. In some instances, the deconvolution matrix comprises a plurality of cell types, each cell type comprising a plurality of expression signature genes, wherein expression counts for each expression signature gene is normalized across the plurality of cell types. In some instances, the deconvolution algorithm identifies and quantifies the at least one cell type that is present in the biological sample using linear least-squares regression (LLSR), quadratic programming (QP), perturbation model for gene expression deconvolution (PERT), robust linear regression (RLR), microarray microdissection with analysis of differences (MMAD), digital sorting algorithm (DSA), or support vector regression. In some instances, the deconvolution algorithm performs an RNA normalization step to compensate for variation in RNA quantity amongst the at least one cell type in order to improve accuracy of the quantified percentage. In some instances, the deconvolution algorithm is a machine learning algorithm trained using comparison data comprising an actual percentage of the at least one cell type. In some instances, the actual percentage is generated using flow cytometry. In some instances, the method further comprises performing next generation RNA sequencing on the biological sample to obtain the RNA expression data and the plurality of expression signature genes. In some instances, the method further comprises obtaining mutational burden data for the biological sample and inputting the mutational burden data into the classifier for analysis in order to enhance classification of the biological sample. In some instances, the classifier is trained on data from no more than 15, 20, 25, 30, 35, 40, 45, or 50 samples and provides an accuracy of at least 70%, 75%, 80%, 85%, 90%, or 95%. In some instances, the accuracy is calculated using a leave-one-out cross-validation method. In some instances, the gene expression data is RNA sequencing data. In some instances, the gene expression data is obtained using next generation sequencing.

The present disclosure also discloses systems comprising for analyzing a biological sample obtained from a subject having a disease or condition, comprising: a database comprising the data set; and at least one computer processor that is coupled to the database, wherein the at least one computer processor is programmed to perform steps comprising: (a) obtaining gene expression data for at least one immune modulatory gene from the biological sample; (b) identifying and quantifying a percentage of at least one cell type that is present in the biological sample based on a plurality of expression signature genes; and (c) using a classifier to analyze the expression of the at least one immune modulatory gene and the percentage of the at least one cell type in order to classify the sample. In some instances, the sample is classified into one of at least two groups. In some instances, the at least two groups comprise a group having a positive response to a therapeutic intervention to the disease or condition and a group having a negative response to the therapeutic intervention. In some instances, the positive response comprises tumor regression, slowing tumor progression, or halt of tumor progression. In some instances, the negative response comprises tumor progression, lack of response to the therapeutic intervention, or a combination thereof In some instances, the therapeutic intervention comprises immunotherapy. In some instances, the immunotherapy comprises a cancer vaccine, cytokine therapy, immune cell therapy, antibody therapy, or any combination thereof In some instances, the therapeutic intervention comprises radiation, chemotherapy, surgery, or a combination thereof. In some instances, the at least one processor is further programmed to provide instructions to start, stop, change, or continue the therapeutic intervention. In some instances, the disease or condition is cancer. In some instances, the at least one cell type comprises at least one immune cell type. In some instances, the at least one immune cell type is selected from the group consisting of CD4+ memory T-cells, CD4+ naive T-cells, CD4+ T-cells, central memory T (Tcm) cells, effector memory T (Tem) cells, CD4+ Tcm, CD4+ Tem, CD8+ T-cells, CD8+ naive T-cells, CD8+ Tcm, CD8+ Tem, regulatory T cells (Tregs), T helper (Th) 1 cells, Th2 cells, gamma delta T (Tgd) cells, natural killer (NK) cells, natural killer T (NKT) cells, B-cells, naive B-cells, memory B-cells, class-switched memory B-cells, pro B-cells, and plasma cells. In some instances, the at least one immune cell type is selected from the group consisting of M1 macrophages, M2 macrophages, CD19+ B cells, CD14+ monocytes, CD56+ NK cells, CD8+ T cells, Treg cells, and CD4+ T cells. In some instances, the at least one immune modulatory gene is selected from the group consisting of CTLA4, OX40, PD-1, IDO1, CD47, PD-L1, TIM-3, BTLA, ICOS, and ARG1. In some instances, the at least one cell type comprises at least 2, 3, 4, 5, 6, 7, or 8 cell types. In some instances, the at least immune modulatory gene comprises at least 2, 3, 4, 5, 6, 7, 8, 9, or 10 genes. In some instances, the classifier is generated using a machine learning algorithm. In some instances, the machine learning algorithm is a random forest algorithm. In some instances, the classifier is trained using data from no more than 50 samples. In some instances, the biological sample comprises cancer or pre-cancer tissue. In some instances, the prediction of an outcome for the subject is a positive response or a negative response to a therapeutic intervention. In some instances, the prediction of an outcome for the subject is a prognosis of the disease or condition. In some instances, the percentage of the at least one cell type is generated using a deconvolution algorithm that applies a deconvolution matrix to RNA sequencing data for the biological sample. In some instances, the deconvolution algorithm applies a deconvolution matrix to the gene expression data to identify and quantify the percentage of the at least one cell type. In some instances, the deconvolution matrix comprises a plurality of immune cell expression signature genes. In some instances, the deconvolution matrix comprises a plurality of tumor cell expression signature genes. In some instances, the deconvolution matrix comprises a plurality of cell types, each cell type comprising a plurality of expression signature genes, wherein expression counts for each expression signature gene is normalized across the plurality of cell types. In some instances, the deconvolution algorithm identifies and quantifies the at least one cell type that is present in the biological sample using linear least-squares regression (LLSR), quadratic programming (QP), perturbation model for gene expression deconvolution (PERT), robust linear regression (RLR), microarray microdissection with analysis of differences (MMAD), digital sorting algorithm (DSA), or support vector regression. In some instances, the deconvolution algorithm performs an RNA normalization step to compensate for variation in RNA quantity amongst the at least one cell type in order to improve accuracy of the quantified percentage. In some instances, the deconvolution algorithm is a machine learning algorithm trained using comparison data comprising an actual percentage of the at least one cell type. In some instances, the actual percentage is generated using flow cytometry. In some instances, the RNA expression data and the plurality of expression signature genes are obtained from the biological sample using next generation RNA sequencing. In some instances, the at least one processor is further programmed to obtain mutational burden data for the biological sample and inputting the mutational burden data into the classifier for analysis in order to enhance classification of the biological sample. In some instances, the classifier is trained on data from no more than 15, 20, 25, 30, 35, 40, 45, or 50 samples and provides an accuracy of at least 70%, 75%, 80%, 85%, 90%, or 95%. In some instances, the accuracy is calculated using a leave-one-out cross-validation method. In some instances, the gene expression data is RNA sequencing data. In some instances, the gene expression data is obtained using next generation sequencing.

Another aspect of the present disclosure provides a non-transitory computer readable medium comprising machine executable code that, upon execution by one or more computer processors, implements any of the methods above or elsewhere herein.

Another aspect of the present disclosure provides a system comprising one or more computer processors and computer memory coupled thereto. The computer memory comprises machine executable code that, upon execution by the one or more computer processors, implements any of the methods above or elsewhere herein.

Additional aspects and advantages of the present disclosure will become readily apparent to those skilled in this art from the following detailed description, wherein only illustrative embodiments of the present disclosure are shown and described. As will be realized, the present disclosure is capable of other and different embodiments, and its several details are capable of modifications in various obvious respects, all without departing from the disclosure. Accordingly, the drawings and description are to be regarded as illustrative in nature, and not as restrictive.

INCORPORATION BY REFERENCE

All publications, patents, and patent applications mentioned in this specification are herein incorporated by reference to the same extent as if each individual publication, patent, or patent application was specifically and individually indicated to be incorporated by reference.

BRIEF DESCRIPTION OF THE DRAWINGS

The patent or application file contains at least one drawing executed in color. Copies of this patent or patent application publication with color drawing(s) will be provided by the Office upon request and payment of the necessary fee.

The novel features of the invention are set forth with particularity in the appended claims. A better understanding of the features and advantages of the present invention will be obtained by reference to the following detailed description that sets forth illustrative embodiments, in which the principles of the invention are utilized, and the accompanying drawings (also “Figure” and “FIG.” herein), of which:

FIG. 1 depicts an example workflow for characterization of a tumor microenvironment.

FIG. 2 depicts an example workflow for cell type and ratio deconvolution.

FIG. 3 depicts a schematic for normalization.

FIG. 4A, FIG. 4B, FIG. 4C, and FIG. 4D depict methods for identifying tumor mutational burden.

FIG. 5A and FIG. 5B depict gene expression levels in glioblastoma.

FIG. 6 depicts gene expression levels in colorectal and blood cancers.

FIG. 7 depicts a report showing immune modulatory molecule expression, mutational burden, and cell deconvolution results.

FIG. 8 schematically illustrates a computer system that is programmed or otherwise configured to implement methods provided herein.

FIG. 9 shows the average amount of total RNA per cell for each immune cell type.

FIG. 10A shows a graph of the observed, expected, and corrected number of M1 macrophages calculated at different dilution points through deconvolution.

FIG. 10B shows a graph of the observed, expected, and corrected number of M2 macrophages calculated at different dilution points through deconvolution.

FIG. 10C shows another graph of the observed, expected, and corrected number of M1 macrophages calculated at different dilution points through deconvolution.

FIG. 10D shows another graph of the observed, expected, and corrected number of M2 macrophages calculated at different dilution points through deconvolution.

FIG. 10E shows another graph of the observed, expected, and corrected number of M1 macrophages calculated at different dilution points through deconvolution.

FIG. 10F shows another graph of the observed, expected, and corrected number of M2 macrophages calculated at different dilution points through deconvolution.

FIG. 11 shows a graph plotting a comparison of known cell percentages to estimated cell percentages obtained using the deconvolution methods described herein.

FIG. 12A shows a bar plot indicating the predictive accuracy of an “escape” biomarker, an “immune” biomarker, and a multi-analyte “paragon” classifier.

FIG. 12B shows box-and-whisker plots that visualize the statistics for groups of samples for the most predictive “escape” biomarker.

FIG. 12C shows box-and-whisker plots that visualize the statistics for groups of samples for the most predictive “immune” biomarker.

FIG. 13 depicts an example flow chart illustrating methods of generating single-analyte and multi-analyte classifiers as described in Example 7.

DETAILED DESCRIPTION

The present disclosure employs, unless otherwise indicated, conventional molecular biology techniques, which are within the skill of the art. Unless defined otherwise, all technical and scientific terms used herein have the same meaning as is commonly understood by one of ordinary skill in the art.

Throughout this disclosure, various embodiments are presented in a range format. It should be understood that the description in range format is merely for convenience and brevity and should not be construed as an inflexible limitation on the scope of any embodiments. Accordingly, the description of a range should be considered to have specifically disclosed all the possible subranges as well as individual numerical values within that range to the tenth of the unit of the lower limit unless the context clearly dictates otherwise. For example, description of a range such as from 1 to 6 should be considered to have specifically disclosed subranges such as from 1 to 3, from 1 to 4, from 1 to 5, from 2 to 4, from 2 to 6, from 3 to 6 etc., as well as individual values within that range, for example, 1.1, 2, 2.3, 5, and 5.9. This applies regardless of the breadth of the range. The upper and lower limits of these intervening ranges may independently be included in the smaller ranges, and are also encompassed within the disclosure, subject to any specifically excluded limit in the stated range. Where the stated range includes one or both of the limits, ranges excluding either or both of those included limits are also included in the disclosure, unless the context clearly dictates otherwise.

The terminology used herein is for the purpose of describing particular embodiments only and is not intended to be limiting of any embodiment. As used herein, the singular forms “a,” “an” and “the” are intended to include the plural forms as well, unless the context clearly indicates otherwise. It will be further understood that the terms “comprises” and/or “comprising,” when used in this specification, specify the presence of stated features, integers, steps, operations, elements, and/or components, but do not preclude the presence or addition of one or more other features, integers, steps, operations, elements, components, and/or groups thereof. As used herein, the term “and/or” includes any and all combinations of one or more of the associated listed items.

The term “ribonucleic acid” or “RNA,” as used herein refers to a molecule comprising at least one ribonucleotide residue. RNA may include transcripts. By “ribonucleotide” is meant a nucleotide with a hydroxyl group at the 2′ position of a beta-D-ribo-furanose moiety. The term RNA includes, but not limited to, mRNA, ribosomal RNA, tRNA, non-protein-coding RNA (npcRNA), non-messenger RNA, functional RNA (fRNA), long non-coding RNA (lncRNA), pre-mRNAs, and primary miRNAs (pri-miRNAs). The term RNA includes, for example, double-stranded (ds) RNAs; single-stranded RNAs; and isolated RNAs such as partially purified RNA, essentially pure RNA, synthetic RNA, recombinant RNA, as well as altered RNA that differ from naturally-occurring RNA by the addition, deletion, substitution and/or alteration of one or more nucleotides. Such alterations can include addition of non-nucleotide material, such as to the end(s) of the siRNA or internally, for example at one or more nucleotides of the RNA. Nucleotides in the RNA molecules described herein can also comprise non-standard nucleotides, such as non-naturally occurring nucleotides or chemically synthesized nucleotides or deoxynucleotides. These altered RNAs can be referred to as analogs or analogs of naturally-occurring RNA.

Unless specifically stated or obvious from context, as used herein, the term “about” in reference to a number or range of numbers is understood to mean the stated number and numbers +/−10% thereof, or 10% below the lower listed limit and 10% above the higher listed limit for the values listed for a range.

The term “sample,” as used herein, generally refers to a biological sample of a subject. The biological sample may be a tissue or fluid of the subject, such as blood (e.g., whole blood), plasma, serum, urine, saliva, mucosal excretions, sputum, stool and tears. The biological sample may be derived from a tissue or fluid of the subject. The biological sample may be a tumor sample or heterogeneous tissue sample. The biological sample may have or be suspected of having disease tissue. The tissue may be processed to obtain the biological sample. The biological sample may be a cellular sample. The biological sample may be a cell-free (or cell free) sample, such as cell-free DNA or RNA. The biological sample may comprise cancer cells, non-cancer cells, immune cells, non-immune cells, or any combination thereof. The biological sample may be a tissue sample. The biological sample may be a liquid sample. The liquid sample can be a cancer or non-cancer sample. Non-limiting examples of liquid biological samples include synovial fluid, whole blood, blood plasma, lymph, bone marrow, cerebrospinal fluid, serum, seminal fluid, urine, and amniotic fluid.

The term “variant,” as used herein, generally refers to a genetic variant, such as an alteration, variant or polymorphism in a nucleic acid sample or genome of a subject. Such alteration, variant or polymorphism can be with respect to a reference genome, which may be a reference genome of the subject or other individual. Single nucleotide polymorphisms (SNPs) are a form of polymorphisms. In some examples, one or more polymorphisms comprise one or more single nucleotide variations (SNVs), insertions, deletions, repeats, small insertions, small deletions, small repeats, structural variant junctions, variable length tandem repeats, and/or flanking sequences. Copy number variants (CNVs), transversions and other rearrangements are also forms of genetic variation. A genomic alternation may be a base change, insertion, deletion, repeat, copy number variation, or transversion.

The term “subject,” as used herein, generally refers to an animal, such as a mammalian species (e.g., human) or avian (e.g., bird) species, or other organism, such as a plant. More specifically, the subject can be a vertebrate, a mammal, a mouse, a primate, a simian or a human. Animals include, but are not limited to, farm animals, sport animals, and pets. The subject can be a healthy individual, an individual that has or is suspected of having a disease or a pre-disposition to the disease, or an individual that is in need of therapy or suspected of needing therapy. The subject can be a patient. The subject may have or be suspected of having a disease.

Generation of Immune-Oncology Profile

Provided herein are systems and methods for generating an immune-oncology profile using sequencing data. The immune-oncology profile often comprises at least one of immune modulatory molecule expression, cell type and ratio, and mutational burden for a given sample. In some cases, sequencing data is used to determine at least one of immune modulatory molecule expression, cell type and ratio, and mutational burden. Systems and methods for determining cell type and ratio may comprise deconvolution methods. An immune-oncology profile comprising immune modulatory molecule expression, cell type and ratio, and mutational burden may be used for therapeutic applications. For example, following determination of immune modulatory molecule expression, cell type and ratio, and mutational burden may provide information for diagnosis or treatment.

A first example workflow process is depicted in FIG. 1. In a first step a formalin-fixed paraffin-embedded (FFPE) sample 101 is provided. RNA extraction 103 is performed followed by sequencing library generation 105. Target gene enrichment 107 is then performed followed by sequencing. Raw sequencing data 109 is generated, which is then used to determine immune modulatory molecule expression 111, cell type and ratio deconvolution 113, and perform mutational burden calculation 115. The immune modulatory molecule expression 111, cell type and ratio deconvolution 113, and mutational burden calculation 115 is then used to generate a report 117 of an immune-oncology profile. An example of a report is illustrated in FIG. 7, showing immune modulatory molecule expression, mutational burden, and cell type and ratio deconvolution results. Expression of immune modulatory or immune escape genes are shown at the top of the report in FIG. 7, which include PD-1, PD-L1, CTLA-4, OX-40, TIM-3, BTLA, ICOS, CD47, IDO1, and ARG1. The “immune deconvolution” section of the report includes a pie chart showing the percentages of general cell types identified in the sample, including 30% immune, 60% tumor, and 5% stromal. More specific breakdowns of the immune cell types and their percentages are shown at the left. The cell types are further divided into categories including T cells (CD4+, CD8+, naïve CD4+, naïve CD8+, Central Memory CD4+, Effector Memory CD4+, Central Memory CD8+, Effector Memory CD8+, and Tregs), CD4+ subtypes (Th1, Th2, Th17), Myeloid cells (monocytic cells, granulocytic cells, macrophages, dendritic cells, MDSC, M1 macrophages, M2 macrophages), NK cells, and B cells (naïve B cells, memory B cells, activated B cells, and plasma B cells). At the bottom of the report is a mutational burden readout. In this case, the mutational burden is provided as a graphic showing a scale between lower mutational burden to the left (left endpoint=0 MutMB) and increasing mutational burden to the right (right endpoint=2000 MutMB), with the circle indicating the sample's mutational burden position on this scale.

Provided herein are systems and methods for generating an immune-oncology profile from a sample of a subject. In some instances, the subject is has or is suspected of having a disease or disorder. In some instances, the immune-oncology profile is used for diagnosing the subject with a disease or disorder. Alternatively or in combination, the immune-oncology profile is used for determining or predicting a response to a therapeutic intervention in the subject.

Generation of an immune-oncology profile as described herein comprises first obtaining a sample from a subject. In some instances, the sample is any fluid or other material derived from the body of a normal or disease subject including, but not limited to, blood, serum, plasma, lymph, urine, saliva, tears, cerebrospinal fluid, milk, amniotic fluid, bile, ascites fluid, organ or tissue extract, and culture fluid in which any cells or tissue preparation from a subject has been incubated. In some instances, the sample is obtained from skin, blood, brain, bladder, bone, bone marrow, breast, colon, stomach, esophagus, ovary, uterus, gallbladder, fallopian tube, testicle, kidney, liver, pancreas, adrenal gland, cervix, endometrium, head or neck, lung, prostate, thymus, thyroid, lymph node, or urinary bladder. In some instances, the sample is a cancer sample. The cancer sample is typically a solid tumor sample or a liquid tumor sample. For example, the cancer sample is obtained from excised tissue. In some instances, the samples, is fresh, frozen, or fixed. In some instances, a fixed sample comprises paraffin-embedded or fixation by formalin, formaldehyde, or gluteraldehyde. In some instances, the sample is formalin-fixed paraffin-embedded.

In some instances, the sample is stored after it has been collected, but before additional steps are to be performed. In some instances, the sample is stored at less than 8° C. In some instances, the sample is stored at less than 4° C. In some instances, the sample is stored at less than 0° C. In some instances, the sample is stored at less than −20° C. In some instances, the sample is stored at less than −70° C. In some instances, the sample is stored a solution comprising glycerol, glycol, dimethyl sulfoxide, growth media, nutrient broth or any combination thereof. The sample may be stored for any suitable period of time. In some instances the sample is stored for any period of time and remains suitable for downstream applications. For example, the sample is stored for any period of time before nucleic acid (e.g., ribonucleic acid (RNA) or deoxyribonucleic acid (DNA)) extraction. In some instances, the sample is stored for at least or about 1 day, 2 day, 3 days, 4 days, 5 days, 6 days, 7 days, 1 week, 2 weeks, 3 weeks, 4 weeks, 1 month, 2 months, 3 months, 4 months, 5 months, 6 months, 7 months, 8 months, 9 months, 10 months, 11 months, 12 months, or more than 12 months. In some instances, the sample is stored for at least 1 year, 2 years, 3, years, 4 years, 5 years, 6 years, 7 years, 8 years, 9 years, 10 years, 11 years, 12 years, or more than 12 years.

Methods and systems as described herein comprise generating an immune-oncology profile from a sample of a subject, wherein the sample comprises a nucleic acid molecule. In some instances, the nucleic acid molecule is RNA, DNA, fragments, or combinations thereof. In some instances, after a sample is obtained, the sample is processed further before analysis. In some instances, the sample is processed to extract the nucleic acid molecule from the sample. In some instances, no extraction or processing procedures are performed on the sample. In some instances, the nucleic acid is extracted using any technique that does not interfere with subsequent analysis. Extraction techniques include, for example, alcohol precipitation using ethanol, methanol or isopropyl alcohol. In some instances, extraction techniques use phenol, chloroform, or any combination thereof. In some instances, extraction techniques use a column or resin based nucleic acid purification scheme such as those commonly sold commercially. In some instances, following extractions, the nucleic acid molecule is purified. In some instances, the nucleic acid molecule is further processed. For example, following extraction and purification, RNA is further reverse transcribed to cDNA. In some instances, processing of the nucleic acid comprises amplification. Following extraction or processing, in some instances, the nucleic acid is stored in water, Tris buffer, or Tris-EDTA buffer before subsequent analysis. In some instances, the sample is stored at less than 8° C. In some instances, the sample is stored at less than 4° C. In some instances, the sample is stored at less than 0° C. In some instances, the sample is stored at less than −20° C. In some instances, the sample is stored at less than −70° C. In some instances, the sample is stored for at least or about 1 day, 2 day, 3 days, 4 days, 5 days, 6 days, 7 days, 1 week, 2 weeks, 3 weeks, 4 weeks, 1 month, 2 months, 3 months, 4 months, 5 months, 6 months, 7 months, 8 months, 9 months, 10 months, 11 months, 12 months, or more than 12 months.

A nucleic acid molecule obtained from a sample comprises may be characterized by factors such as integrity of the nucleic acid molecule or size of the nucleic acid molecule. In some instances, the nucleic acid molecule is DNA. In some instances, the nucleic acid molecule is RNA. In some instances, the RNA or DNA comprises a specific integrity. For example, the RNA integrity number (RIN) of the RNA is no more than about 2. In some instances, the RNA molecules in a sample have a RIN of about 2 to about 10. In some instances, the RNA molecules in a sample have a RIN of at least about 2. In some instances, the RNA molecules in a sample have a RIN of at most about 10. In some instances, the RNA molecules in a sample have a RIN of about 2 to about 3, about 2 to about 4, about 2 to about 5, about 2 to about 6, about 2 to about 7, about 2 to about 8, about 2 to about 9, about 2 to about 10, about 3 to about 4, about 3 to about 5, about 3 to about 6, about 3 to about 7, about 3 to about 8, about 3 to about 9, about 3 to about 10, about 4 to about 5, about 4 to about 6, about 4 to about 7, about 4 to about 8, about 4 to about 9, about 4 to about 10, about 5 to about 6, about 5 to about 7, about 5 to about 8, about 5 to about 9, about 5 to about 10, about 6 to about 7, about 6 to about 8, about 6 to about 9, about 6 to about 10, about 7 to about 8, about 7 to about 9, about 7 to about 10, about 8 to about 9, about 8 to about 10, or about 9 to about 10. The RNA molecule in a sample may be characterized by size. In some instances, at least 10%, 20%, 30%, 40%, 50%, 60%, 70%, 80%, or 90%, or more of the RNA molecules in a sample are at least 150, 175, 200, 225, 250, 275, 300, 325, 350, 375, 400, or more than 400 nucleotides in size. In some instances, the RNA molecules in the sample are at least 200 nucleotides in size. In some instances, the RNA molecules of at least 200 nucleotides in size comprise a percentage of the sample (DV200). For example, the percentage is at least or about 40%, 45%, 50%, 55%, 60%, 65%, 70%, 75%, 80%, 85%, 90%, 95%, or more than 95%. In some instances, the RNA molecules in a sample have a DV200 value of about 10% to about 90%. In some instances, the RNA molecules in a sample have a DV200 value of at least about 10%. In some instances, the RNA molecules in a sample have a DV200 value of at most about 90%. In some instances, the RNA molecules in a sample have a DV200 value of about 10% to about 20%, about 10% to about 30%, about 10% to about 40%, about 10% to about 50%, about 10% to about 60%, about 10% to about 70%, about 10% to about 80%, about 10% to about 90%, about 20% to about 30%, about 20% to about 40%, about 20% to about 50%, about 20% to about 60%, about 20% to about 70%, about 20% to about 80%, about 20% to about 90%, about 30% to about 40%, about 30% to about 50%, about 30% to about 60%, about 30% to about 70%, about 30% to about 80%, about 30% to about 90%, about 40% to about 50%, about 40% to about 60%, about 40% to about 70%, about 40% to about 80%, about 40% to about 90%, about 50% to about 60%, about 50% to about 70%, about 50% to about 80%, about 50% to about 90%, about 60% to about 70%, about 60% to about 80%, about 60% to about 90%, about 70% to about 80%, about 70% to about 90%, or about 80% to about 90%.

In some instances, after the samples have been obtained and nucleic acid molecule isolated, the nucleic acid molecule is prepared for sequencing. In some instances, a sequencing library is prepared. Numerous library generation methods have been described. In some instances, methods for library generation comprise addition of a sequencing adapter. Sequencing adapters may be added to the nucleic acid molecule by ligation. In some instances, library generation comprises an end-repair reaction.

Sometimes, library generation for sequencing comprises an enrichment step. For example, coding regions of the mRNA are enriched. In some instances, the enrichment step is for a subset of genes. In some instances, the enrichment step comprises using a bait set. The bait set may be used to enrich for genes used for specific downstream applications. A bait set generally refers to a set of baits targeted toward a selected set of genomic regions of interest. For example, a bait set may be selected for genomic regions relating to at least one of immune modulatory molecule expression, cell type and ratio, or mutational burden. In some instances, one bait set is used for determining immune modulatory molecule expression, a second bait set is used for determining cell type and ratio, and a third bait set is used for determining mutational burden. In some instances, the same bait set is used for determining immune modulatory molecule expression, cell type and ratio, mutational burden, or combinations thereof. In some instances, a bait set comprises at least one unique molecular identifier (UMI). The term “unique molecular identifier (UMI)” or “UMI” as used herein refers to nucleic acid having a sequence which can be used to identify and/or distinguish one or more first molecules to which the UMI is conjugated from one or more second molecules. In some instances, the UMI is conjugated to one or more target molecules of interest or amplification products thereof. UMIs may be single or double stranded.

The systems and methods disclosed herein provide for the sequencing for a number of genes. In some instances, the number of genes is at least about 200, 300, 400, 500, 600, 700, 800, 900, 1000, 1500, 2000, 2500, 3000, 3500, 4000, 4500, 5000, 5500, 6000, 6500, 7000, 7500, 8000, 8500, 9000, 9500, 10000, or more than 10000 genes. In some instances, the number of genes to be sequenced is in a range of about 500 to about 1000 genes. In some instances, the number of genes to be sequenced is in a range of about at least 200. In some instances, the number of genes to be sequenced is in a range of about at most 10,000. In some instances, the number of genes to be sequenced is in a range of about 200 to 500, 200 to 1,000, 200 to 2,000, 200 to 4,000, 200 to 6,000, 200 to 8,000, 200 to 10,000, 500 to 1,000, 500 to 2,000, 500 to 4,000, 500 to 6,000, 500 to 8,000, 500 to 10,000, 1,000 to 2,000, 1,000 to 4,000, 1,000 to 6,000, 1,000 to 8,000, 1,000 to 10,000, 2,000 to 4,000, 2,000 to 6,000, 2,000 to 8,000, 2,000 to 10,000, 4,000 to 6,000, 4,000 to 8,000, 4,000 to 10,000, 6,000 to 8,000, 6,000 to 10,000, or 8,000 to 10,000. Examples of genes to be sequenced are seen in Tables 1A-1E or Table 5.

Sequencing may be performed with any appropriate sequencing technology. Examples of sequencing methods include, but are not limited to single molecule real-time sequencing, Polony sequencing, sequencing by ligation, reversible terminator sequencing, proton detection sequencing, ion semiconductor sequencing, nanopore sequencing, electronic sequencing, pyrosequencing, Maxam-Gilbert sequencing, chain termination (e.g., Sanger) sequencing, +S sequencing, or sequencing by synthesis.

Sequencing methods may include, but are not limited to, one or more of: high-throughput sequencing, pyrosequencing, sequencing-by-synthesis, single-molecule sequencing, nanopore sequencing, semiconductor sequencing, sequencing-by-ligation, sequencing-by-hybridization, RNA-Seq (Illumina), Digital Gene Expression (Helicos), Next generation sequencing, Single Molecule Sequencing by Synthesis (SMSS) (Helicos), massively-parallel sequencing, Clonal Single Molecule Array (Solexa), shotgun sequencing, Maxim-Gilbert sequencing, and primer walking. Sequencing may generate sequencing reads (“reads”), which may be processed (e.g., alignment) to yield longer sequences, such as consensus sequences. Such sequences may be compared to references (e.g., a reference genome or control) to identify variants, for example.

An average read length from sequencing may vary. In some instances, the average read length is at least about 100, 200, 300, 400, 500, 600, 700, 800, 900, 1000, 2000, 3000, 4000, 5000, 6000, 7000, 8000, 9000, 10000, 20000, 30000, 40000, 50000, 60000, 70000, 80000, or more than 80000 base pairs. In some instances, the average read length is in a range of about 100 to 80,000. In some instances, the average read length is in a range of about at least 100. In some instances, the average read length is in a range of about at most 80,000. In some instances, the average read length is in a range of about 100 to 200, 100 to 300, 100 to 500, 100 to 1,000, 100 to 2,000, 100 to 4,000, 100 to 8,000, 100 to 10,000, 100 to 20,000, 100 to 40,000, 100 to 80,000, 200 to 300, 200 to 500, 200 to 1,000, 200 to 2,000, 200 to 4,000, 200 to 8,000, 200 to 10,000, 200 to 20,000, 200 to 40,000, 200 to 80,000, 300 to 500, 300 to 1,000, 300 to 2,000, 300 to 4,000, 300 to 8,000, 300 to 10,000, 300 to 20,000, 300 to 40,000, 300 to 80,000, 500 to 1,000, 500 to 2,000, 500 to 4,000, 500 to 8,000, 500 to 10,000, 500 to 20,000, 500 to 40,000, 500 to 80,000, 1,000 to 2,000, 1,000 to 4,000, 1,000 to 8,000, 1,000 to 10,000, 1,000 to 20,000, 1,000 to 40,000, 1,000 to 80,000, 2,000 to 4,000, 2,000 to 8,000, 2,000 to 10,000, 2,000 to 20,000, 2,000 to 40,000, 2,000 to 80,000, 4,000 to 8,000, 4,000 to 10,000, 4,000 to 20,000, 4,000 to 40,000, 4,000 to 80,000, 8,000 to 10,000, 8,000 to 20,000, 8,000 to 40,000, 8,000 to 80,000, 10,000 to 20,000, 10,000 to 40,000, 10,000 to 80,000, 20,000 to 40,000, 20,000 to 80,000, or 40,000 to 80,000.

In some instances, a number of nucleotides that are sequenced are at least or about 5, 10, 15, 20, 25, 30, 35, 40, 45, 50, 100, 150, 200, 300, 400, 500, 2000, 2500, 3000, or more than 3000 nucleotides. In some instances, the number of nucleotides that are sequenced are about 5 to about 3,000 nucleotides. In some instances, the number of that are sequenced are at least 5 nucleotides. In some instances, the number of nucleotides that are sequenced are at most 3,000 nucleotides. In some instances, the number of nucleotides that are sequenced are 5 to 50, 5 to 100, 5 to 200, 5 to 400, 5 to 600, 5 to 800, 5 to 1,000, 5 to 1,500, 5 to 2,000, 5 to 2,500, 5 to 3,000, 50 to 100, 50 to 200, 50 to 400, 50 to 600, 50 to 800, 50 to 1,000, 50 to 1,500, 50 to 2,000, 50 to 2,500, 50 to 3,000, 100 to 200, 100 to 400, 100 to 600, 100 to 800, 100 to 1,000, 100 to 1,500, 100 to 2,000, 100 to 2,500, 100 to 3,000, 200 to 400, 200 to 600, 200 to 800, 200 to 1,000, 200 to 1,500, 200 to 2,000, 200 to 2,500, 200 to 3,000, 400 to 600, 400 to 800, 400 to 1,000, 400 to 1,500, 400 to 2,000, 400 to 2,500, 400 to 3,000, 600 to 800, 600 to 1,000, 600 to 1,500, 600 to 2,000, 600 to 2,500, 600 to 3,000, 800 to 1,000, 800 to 1,500, 800 to 2,000, 800 to 2,500, 800 to 3,000, 1,000 to 1,500, 1,000 to 2,000, 1,000 to 2,500, 1,000 to 3,000, 1,500 to 2,000, 1,500 to 2,500, 1,500 to 3,000, 2,000 to 2,500, 2,000 to 3,000, or 2,500 to 3,000 nucleotides.

Sequencing methods may include a barcoding or “tagging” step. In some instances barcoding (or “tagging”) can allow for generation of a population of samples of nucleic acids, wherein each nucleic acid can be identified from which sample the nucleic acid originated. In some instances, the barcode comprises oligonucleotides that are ligated to the nucleic acids. In some instances, the barcode is ligated using an enzyme, including but not limited to, E. coli ligase, T4 ligase, mammalian ligases (e.g., DNA ligase I, DNA ligase II, DNA ligase III, DNA ligase IV), thermostable ligases, and fast ligases.

Barcoding or tagging may occur using various types of barcodes or tags. Examples of barcodes or tags include, but are not limited to, a radioactive barcode or tag, a fluorescent barcode or tag, an enzyme, a chemiluminescent barcode or tag, and a colorimetric barcode or tag. In some instances, the barcode or tag is a fluorescent barcode or tag. In some instances, the fluorescent barcode or tag comprises a fluorophore. In some instances, the fluorophore is an aromatic or heteroaromatic compound. In some instances, the fluorophore is a pyrene, anthracene, naphthalene, acridine, stilbene, benzoxaazole, indole, benzindole, oxazole, thiazole, benzothiazole, canine, carbocyanine, salicylate, anthranilate, xanthenes dye, coumarin. Examples of xanthene dyes include, e.g., fluorescein and rhodamine dyes. Fluorescein and rhodamine dyes include, but are not limited to 6-carboxyfluorescein (FAM), 2′7′-dimethoxy-4′5′-dichloro-6-carboxyfluorescein (JOE), tetrachlorofluorescein (TET), 6-carboxyrhodamine (R6G), N,N,N,N′-tetramethyl-6-carboxyrhodamine (TAMRA), 6-carboxy-X-rhodamine (ROX). In some instances, the fluorescent barcode or tag also includes the naphthylamine dyes that have an amino group in the alpha or beta position. For example, naphthylamino compounds include 1-dimethylaminonaphthyl-5-sulfonate, 1-anilino-8-naphthalene sulfonate and 2-p-toluidinyl-6-naphthalene sulfonate, 5-(2′-aminoethyl)aminonaphthalene-1-sulfonic acid (EDANS). Examples of coumarins include, e.g., 3-phenyl-7-isocyanatocoumarin; acridines, such as 9-isothiocyanatoacridine and acridine orange; N-(p-(2-benzoxazolyl)phenyl) maleimide; cyanines, such as, e.g., indodicarbocyanine 3 (Cy3), indodicarbocyanine 5 (Cy5), indodicarbocyanine 5.5 (Cy5.5), 3-(-carboxy-pentyl)-3′-ethyl-5,5′-dimethyloxacarbocyanine (CyA); 1H, 5H, 11H, 15H-Xantheno[2,3, 4-ij: 5,6,7-i′j′]diquinolizin-18-ium, 9-[2 (or 4)-[[[6-[2,5-dioxo-1-pyrrolidinyl)oxy]-6-oxohexyl]amino]sulfonyl]-4 (or 2)-sulfophenyl]-2,3, 6,7, 12,13, 16,17-octahydro-inner salt (TR or Texas Red); or BODIPY™ dyes.

In some instances, a different barcode or tag is supplied a sample comprising nucleic acids. Examples of barcode lengths include barcode sequences comprising, without limitation, about 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 15, 20, 25 or more bases in length. Examples of barcode lengths include barcode sequences comprising, without limitation, from 1-5, 1-10, 5-20, or 1-25 bases in length. Barcode systems may be in base 1, 2, 3, 4, 5, 6, 7, 8, 9, or 10 or a similar coding scheme. In some instances, a number of barcodes is at least or about 1, 2, 3, 4, 5, 6, 7, 8, 9,10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 25, 50, 100, 200, 300, 400, 500, 600, 700, 800, 900, 1000, 2000, 4000, 6000, 8000, 10000, 12000, 14000, 16000, 18000, 20000, 25000, 30000, 40000, 50000, 100000, 500000, 1000000, or more than 1000000 barcodes. In some instances, a number of barcodes is in a range of 1-1000000 barcodes. In some instances, the number of barcodes is in a range of about 1-10 1-50 1-100 1-500 1-1000 1-5,000 1-10000 1-50000 1-100000 1-500000 1-1000000 10-50 10-100 10-500 10-1000 10-5,000 10-10000 10-50000 10-100000 10-500000 10-1000000 50-100 50-500 50-1000 50-5,000 50-10000 50-50000 50-100000 50-500000 50-1000000 100-500 100-1000 100-5,000 100-10000 100-50000 100-100000 100-500000 100-1000000 500-1000 500-5,000 500-10000 500-50000 500-100000 500-500000 500-1000000 1000-5,000 1000-10000 1000-50000 1000-100000 1000-500000 1000-1000000 5,000-10000 5,000-50000 5,000-100000 5,000-500000 5,000-1000000 10000-50000 10000-100000 10000-500000 10000-1000000 50000-100000 50000-500000 50000-1000000 100000-500000 100000-1000000 or 500000-1000000 barcodes.

Following sequencing of a sample, sequencing data as described herein can be used for at least one of determining immune modulatory molecule expression, performing cell type and ratio deconvolution, and calculating mutational burden. An example of a workflow is seen in FIG. 2. Referring to FIG. 2, sequencing data is used to determine tumor expression counts 201 and immune cell expression signatures 203. The tumor expression counts 201 and immune cell expression signatures 203 are then subjected to a deconvolution algorithm 205 to calculate immune cell percentage 207.

Sequencing data as provided herein are used to determine gene expression. In some instances, the sequencing data is obtained from sequencing RNA from a sample. In some instances, the gene expression is of an immune modulatory molecule such as an immune checkpoint molecule or immune inhibitory molecule. Examples of immune modulatory molecules include, but are not limited to, one or more of 2B4 (CD244), A2aR, B7H3 (CD276), B7H4 (VTCN1), B7H6, B7RP1, BTLA (CD272), butyrophilins, CD103, CD122, CD137 (4-1BB), CD137L, CD160, CD2, CD200R, CD226, CD26, CD27, CD28, CD30, CD39, CD40, CD48, CD70, CD73, CD80 (B7.1), CD86 (B7.2), CEACAM1, CGEN-15049, CTLA-4, DR3, GAL9, GITR, GITRL, HVEM, ICOS, ICOSL (B7H2), IDO1, IDO2, ILT-2 (LILRB1), ILT-4 (LILRB2), KIR, KLRG1, LAG3, LAIR1 (CD305), LIGHT (TNFSF14), MARCO, NKG2A, NKG2D, OX-40, OX-40L, PD-1, PDL-1 (B7-H1, CD 274), PDL-2 (B7-DC, CD 273), PS, SIRPalpha (CD47), SLAM, TGFR, TIGIT, TIM1, TIM3 (HAVCR2), TIM4, or VISTA.

In some instances, the gene expression of a sample is compared to a reference sample. Sometimes, the systems and methods disclosed herein generate an immune-oncology profile comprising a visual representation of immune modulatory molecule gene expression. In some cases, the visual representation presents the gene expression of one or more immune modulatory molecules relative to a reference expression level. In some instances, the reference expression level is obtained from a reference sample. Sometimes, the reference sample comprises the same cell or tissue type as the sample being evaluated for gene expression. Sometimes, the gene expression of a sample is compared to an averaged or plurality of reference samples. As an example, a cancer sample being evaluated for gene expression is compared to average gene expression for reference samples of the same cancer type as the cancer sample in a reference database (e.g., TCGA database).

Provided herein are systems and methods for generating an immune-oncology profile comprising determining cell type and ratio in a sample using sequencing data. The sample often comprises a heterogeneous composition of different cell types and/or subtypes. Sometimes, the sample is a tumor sample. The cell types and/or subtypes that make up the sample includes one or more of cancer cells, non-cancer cells, and/or immune cells. Examples of non-immune cells include salivary gland cells, mammary gland cells, lacrimal gland cells, ceruminous gland cells, eccrine sweat gland cells, apocrine sweat gland cells, sebaceous gland cells, Bowman's gland cells, Brunner's gland cells, prostate gland cells, seminal vesicle cells, bulbourethral gland cells, keratinizing epithelial cells, hair shaft cells, epithelial cells, exocrine secretory epithelial cells, uterus endometrium cells, isolated goblet cells of respiratory and digestive tracts, stomach lining mucous cells, hormone secreting cells, pituitary cells, gut and respiratory tract cells, thyroid gland cells, adrenal gland cells, chromaffin cells, Leydig cells, theca interna cells, macula densa cells of kidney, peripolar cells of kidney, mesangial cells of kidney, hepatocytes, white fat cells, brown fat cells, liver lipocytes, kidney cells, kidney glomerulus parietal cells, kidney glomerulus podocytes, kidney proximal tubule brush border cells, loop of Henle thin segment cells, kidney distal tubule cells, endothelial fenestrated cells, vascular endothelial continuous cells, synovial cells, serosal cells, squamous cells, columnar cells of endolymphatic sac with microvilli, columnar cells of endolymphatic sac without microvilli, vestibular membrane cells, stria vascularis basal cells, stria vascularis marginal cells, choroid plexus cells, respiratory tract ciliated cells, oviduct ciliated cells, uterine endometrial ciliated cells, rete testis ciliated cells, ductulus efferens ciliated cells, ciliated ependymal cells of central nervous system, organ of Corti interdental epithelial cells, loose connective tissue fibroblasts, corneal fibroblasts, tendon fibroblasts, bone marrow reticular tissue fibroblasts, other nonepithelial fibroblasts, pericytes, skeletal muscle cells, red skeletal muscle cells, white skeletal muscle cells, intermediate skeletal muscle cells, nuclear bag cells of muscle spindle, nuclear chain cells of muscle spindle, satellite cells, cardiac muscle cells, ordinary cardiac muscle cells, nodal cardiac muscle cells, purkinje fiber cells, smooth muscle cells, myoepithelial cells of iris, myoepithelial cells of exocrine glands, erythrocytes, megakaryocytes, monocytes, epidermal Langerhans cells, osteoclasts, sensory neurons, olfactory receptor neurons, pain-sensitive primary sensory neurons, photoreceptor cells of retina in eye, photoreceptor rod cells, proprioceptive primary sensory neurons (various types), touch-sensitive primary sensory neurons, taste bud cells, autonomic neuron cells, Schwann cells, satellite cells, glial cells, astrocytes, oligodendrocytes, melanocytes, germ cells, nurse cells, interstitial cells, and pancreatic duct cells. Various cell types may be determined for the sample using methods as described herein including, but not limited to, lymphoid cells, stromal cells, stem cells, and myeloid cells. Examples of lymphoid cells include, but are not limited to, CD4+ memory T-cells, CD4+ naive T-cells, CD4+ T-cells, central memory T (Tcm) cells, effector memory T (Tem) cells, CD4+ Tcm, CD4+ Tem, CD8+ T-cells, CD8+ naive T-cells, CD8+ Tcm, CD8+ Tem, regulatory T cells (Tregs), T helper (Th) 1 cells, Th2 cells, gamma delta T (Tgd) cells, natural killer (NK) cells, natural killer T (NKT) cells, B-cells, naive B-cells, memory B-cells, class-switched memory B-cells, pro B-cells, and plasma cells. In some instances, the cells are stromal cells, for example, mesenchymal stem cells, adipocytes, preadipocytes, stromal cells, fibroblasts, pericytes, endothelial cells, microvascular endothelial cells, lymphatic endothelial cells, smooth muscle cells, chondrocytes, osteoblasts, skeletal muscle cells, myocytes. Examples of stem cells include, but are not limited to, hematopoietic stem cells, common lymphoid progenitor cells, common myeloid progenitor cells, granulocyte-macrophage progenitor cells, megakaryocyte-erythroid progenitor cells, multipotent progenitor cells, megakaryocytes, erythrocytes, and platelets. Examples of myeloid cells include, but are not limited to, monocytes, macrophages, macrophages M1, macrophages M2, dendritic cells, conventional dendritic cells, plasmacytoid dendritic cells, immature dendritic cells, neutrophils, eosinophils, mast cells, and basophils. Other cell types may be determined using methods as described herein, for example, epithelial cells, sebocytes, keratinocytes, mesangial cells, hepatocytes, melanocytes, keratocytes, astrocytes, and neurons.

In some instances, the sequencing data is used to determine immune cell expression. Examples of immune cells to be detected by methods described herein include, but are not limited to, CD4+ memory T-cells, CD4+ naive T-cells, CD4+ T-cells, central memory T (Tcm) cells, effector memory T (Tem) cells, CD4+ Tcm, CD4+ Tem, CD8+ T-cells, CD8+ naive T-cells, CD8+ Tcm, CD8+ Tem, regulatory T cells (Tregs), T helper (Th) 1 cells, Th2 cells, gamma delta T (Tgd) cells, natural killer (NK) cells, natural killer T (NKT) cells, B-cells, naive B-cells, memory B-cells, class-switched memory B-cells, pro B-cells, and plasma cells. In some instances, the sequencing data is used to determine expression of non-immune cells including, but not limited to, stromal cells, stem cells, or tumor cells.

Methods and systems for determining cell type and ratio may comprise determining gene expression. In some instances, determining cell type and ratio may further comprise methods relating to deconvolution. In some instances, a deconvolution matrix is used. The deconvolution matrix typically comprises gene expression for one or more cell types. In some instances, the matrix is used for a complex data set of RNA sequencing gene expression data to allow for identification of cell types in the data and the relative proportions of each cell type. See FIG. 3. In some instances, individual cell types/subtypes and the relative proportion of these individual cell types/subtypes are determined from sequencing data using a deconvolution matrix. In some cases, the relative proportion of at least 2 cell types/subtypes, at least 3 cell types/subtypes, at least 4 cell types/subtypes, at least 5 cell types/subtypes, at least 6 cell types/subtypes, at least 7 cell types/subtypes, at least 8 cell types/subtypes, at least 9 cell types/subtypes, at least 10 cell types/subtypes, at least 11 cell types/subtypes, at least 12 cell types/subtypes, at least 13 cell types/subtypes, at least 14 cell types/subtypes, at least 15 cell types/subtypes, at least 16 cell types/subtypes, at least 17 cell types/subtypes, at least 18 cell types/subtypes, at least 19 cell types/subtypes, at least 20 cell types/subtypes, at least 21 cell types/subtypes, at least 22 cell types/subtypes, at least 23 cell types/subtypes, or at least 24 cell types are determined from sequencing data using a deconvolution matrix. A matrix equation illustrates the mathematical relationship between a matrix comprising expression signatures of individual cell types, the percentage of each cell type, and the bulk expression counts. In some instances, the matrix equation is Ax=b, where A is the cell expression fingerprints (i.e., deconvolution matrix), x is the cell percentages, and b is the bulk expression counts. In some instances, the matrix equation is solved by methods such as matrix algebra, regression analysis, and/or machine learning. Alternately or in combination, deconvolution methods comprise linear least-squares regression (LLSR), quadratic programming (QP), perturbation model for gene expression deconvolution (PERT), robust linear regression (RLR), microarray microdissection with analysis of differences (MMAD), digital sorting algorithm (DSA), or support vector regression (SVR). In some instances, deconvolution comprises a normalization step. Referring to FIG. 3, normalization may occur across a row or down a column. For example, normalization occurs across a row, wherein the row includes distinct cell types or down a column, wherein the column includes gene expression of cells for a specific cell type. In some instances, normalization occurs across a row. In some instances, cell fractions are considered in determining gene expression (FIG. 3). In some instances, a deconvolution matrix is generated for each type of sample analyzed. For example, certain cell types have a different gene expression signature depending on the local tissue environment. As a result, a one-size-fits-all deconvolution matrix is sometimes less accurate than a deconvolution matrix “tailored” to a specific sample type. In some instances, the deconvolution algorithm maintains a database comprising a plurality of deconvolution matrices. In some instances, the deconvolution algorithm selects a deconvolution matrix for analyzing the gene expression data of a sample based on the sample type. The use of a tailored deconvolution matrix enables the use of a narrower set of genes for deconvolution of the sample. The narrower set of genes can increase speed of analysis and the number of samples that are processed at one time. In some instances, a smaller capture or bait set is used to enrich for the narrower set of genes for downstream analysis (e.g., RNA-Seq).

Methods and systems for determining cell type and ratio comprising methods relating to deconvolution may further comprise normalizing RNA content. In some instances, the RNA content is normalized or corrected based on cell type. For example, RNA content is normalized based on the amount of RNA in an individual cell type. In some instances, normalizing RNA content comprises determining a number of cells used to generate the RNA. In some instances, the number of cells is determined by flow cytometry, manual cell counting, automated cell counting, microscopy, or spectrophotometry. In some instances, the number of cells is at least or about 30,000, 40,000, 50,000, 60,000, 70,000, 80,000, 90,000, 100,000, 200,000, 300,000, 400,000, 500,000, 600,000, 700,000, 800,000, 900,000, 1 million, 2 million, 3 million, 4 million, or more than 4 million cells.

Following determination of RNA content for an individual cell type, a correction value may be determined. In some instances, the cell is an immune cell. Examples of immune cells include, but are not limited to, a CD4+ T cell, a CD8+ T cell, a monocyte, a B-cell, a natural killer cell (NK), a M1 macrophage, or a M2 macrophage. In some instances, the immune cell is a CD4+ T cell. In some instances, a correction value for each individual cell type is determined. For example, the cell correction value for CD4+ T cell is about 1.00. Sometimes, the cell correction value for CD4+ T cell is from 0.9 to 1.1. In some instances, the cell correction value for CD8+ T cell is about 1.03. Sometimes, the cell correction value for CD8+ T cell is from 0.93 to 1.13. In some instances, the cell correction value for a monocyte is about 1.35. Sometimes, the cell correction value for a monocyte is from 1.25 to 1.45. In some instances, the cell correction value for a B-cell is about 0.53. Sometimes, the cell correction value for a B-cell is from 0.43 to 0.63. In some instances, the cell correction value for a natural killer cell (NK) is about 0.47. Sometimes, the cell correction value for a NK cell is from 0.37 to 0.57. In some instances, the cell correction value for a M1 macrophage is about 7.59. Sometimes, the cell correction value for a M1 macrophage is from 6.59 to 8.59. In some instances, the cell correction value for a M2 macrophage is about 12.26. Sometimes, the cell correction value for a M2 macrophage is from 11.26 to 13.26.

The correction value may be used to identify cell percentages of individual cell types. In some instances, the correction value is used in combination with deconvolution methods to determine cell percentages of individual cell types. In some instances, the correction value is applied prior to deconvolution methods. For example, the correction value is applied prior to support vector regression of RNA sequence data. In some instances, the correction value is applied following support vector regression and the cell types have been deconvoluted.

Methods and systems for determining cell type and ratio comprising methods relating to deconvolution and normalizing RNA content may result in an accurate determination of immune cell type percentages in a sample. In some instances, the accuracy is at least or about 20%, 25%, 30%, 35%, 40%, 45%, 50%, 60%, 70%, 80%, 90%, 95%, or more than 95% improved using methods and systems as described herein as compared to methods and systems where RNA content is not normalized.

An immune-oncology profile may comprise the cell types and ratios present in a sample using deconvolution of expression data for a plurality of genes. The genes typically exhibit differential expression in at least two cell types that are evaluated using deconvolution. In some cases, the genes exhibit differential expression between cancer and non-cancer cells, between different types of cancer cells, between immune and non-immune cells, between different types of immune cells, between different types of non-cancer cells, or any combination thereof. Examples of genes for inclusion in a deconvolution matrix include those listed in Tables 1A-1E. In some instances, a deconvolution matrix comprises at least about 10, 20, 30, 40, 50, 100, 150, 200, 250, 300, 350, 400, 450, 500, 650, 700, 750, 800, 850, 900, 950, 1000, 1500, 2000, 2500, 3000, or more than 3000 genes. In some instances, a deconvolution matrix comprises no more than about 10, 20, 30, 40, 50, 100, 150, 200, 250, 300, 350, 400, 450, 500, 650, 700, 750, 800, 850, 900, 950, 1000, 1500, 2000, 2500, or about 3000 genes. In some instances, a deconvolution matrix comprises a number of genes in a range of about 50 to 100, 50 to 200, 50 to 300, 50 to 400, 50 to 500, 50 to 600, 50 to 700, 50 to 800, 50 to 900, 50 to 1,000, 50 to 1,500, 100 to 200, 100 to 300, 100 to 400, 100 to 500, 100 to 600, 100 to 700, 100 to 800, 100 to 900, 100 to 1,000, 100 to 1,500, 200 to 300, 200 to 400, 200 to 500, 200 to 600, 200 to 700, 200 to 800, 200 to 900, 200 to 1,000, 200 to 1,500, 300 to 400, 300 to 500, 300 to 600, 300 to 700, 300 to 800, 300 to 900, 300 to 1,000, 300 to 1,500, 400 to 500, 400 to 600, 400 to 700, 400 to 800, 400 to 900, 400 to 1,000, 400 to 1,500, 500 to 600, 500 to 700, 500 to 800, 500 to 900, 500 to 1,000, 500 to 1,500, 600 to 700, 600 to 800, 600 to 900, 600 to 1,000, 600 to 1,500, 700 to 800, 700 to 900, 700 to 1,000, 700 to 1,500, 800 to 900, 800 to 1,000, 800 to 1,500, 900 to 1,000, 900 to 1,500, or 1,000 to 1,500 genes. In some instances, a deconvolution matrix comprises at least about 10, 20, 30, 40, 50, 60, 70, 80, 90, 100, 110, or about 120 genes from Tables 1A-1E. In some instances, a deconvolution matrix comprises no more than about 10, 20, 30, 40, 50, 60, 70, 80, 90, 100, 110, or about 120 genes from Tables 1A-1E.

TABLE 1A Deconvolution Genes for CD4+ T-cells ALS2CL ANKRD55 ZNF483 TRAV13-1 ST6GALNAC1 SEMA3A TRBV5-4 DNAH8 IL2RA TRBV11-2 TRAV8-2 KRT72 EPPK1 FAM153B TRAV12-2 TRAV8-6 TRBV6-5 TRAV10 IGKV5-2 IGLV6-57 TRAV12-1 CTLA4 TSHZ2 FOXP3 IGHV4-28 TRAV2 SORCS3 TRAV5 MDS2 NTN4 IGLV10-54 DACT1 TRBV5-5 THEM5 HPCAL4 CD4

TABLE 1B Deconvolution Genes for CD8+ T-cells FLT4 TRBV4-2 TRBV6-4 SPRY2 S100B TNIP3 CD248 ROBO1 CD8B TRBV2 CYP4F22 PZP LAG3 KLRC4-KLRK1 CRTAM SHANK1 ANAPC1P1 NRCAM JAKMIP1 KLRC2 KLRC3 CD8A TRAV4 FBLN2

TABLE 1C Deconvolution Genes for Monocytes DES HLX FPR3 FCGR1B LOXHD1 EPHB2 LPL LIPN AQP9 MILR1 RETN GPNMB CYP2S1 PDK4 LILRA6 SEPT10 PLA2G4A FOLR2 FOLR3 C1QB SLC6A12 SLC22A16 DOCK1 NRG1 RXFP2 RIN2 ARHGEF10L LPAR1 CES1 FPR2

TABLE 1D Deconvolution Genes for NK cells IGFBP7 LDB2 GUCY1A3 KLRF1 DTHD1 AKR1C3 FASLG KLRC1 XCL1 DAB2 FAT4 CD160 BNC2 CXCR1 SIGLEC17P SH2D1B DGKK ZMAT4 LGALS9B NMUR1 LGALS9C MLC1 LIM2 NCR1 CCNJL PCDH1

TABLE 1E Deconvolution Genes for B-cells UGT8 IGKV1OR2-108 IGHE SCN3A IGLV2-8 IGKV1D-16 MYO5B ENAM RP11-148O21.2 IGLC7 IGHV1-2 IGKJ5 SOX5 TNFRSF13B IGKV2D-29 IGKV1-17 IGLV2-18 IGHV2-70 CHL1 IGKV3D-20 IGLV8-61 IGKV6-21

There are potentially around 19,700 possible gene identifiers that can be used from the transcriptome for generating a basis or deconvolution matrix. In some instances, genes are selected for deconvolution if the genes are differentially expressed in pairwise cell type differential expression analysis. In some instances, genes are selected for deconvolution if the genes are expressed at a consistent level within a cell type across samples. The present disclosure has identified a small subset of the transcriptome as being useful for carrying out deconvolution of immune cell types. Table 2 shows a list of 293 total genes and corresponding Ensembl gene identifiers in a 15 differentially expressed gene list. The genes in Table 2 are generated by performing pairwise comparisons for each cell type and tallying up the top 15 differentially expressed genes in each comparison. Tables 3 and 4 show genes generated using this same approach with Table 3 showing a 10 differentially expressed gene list (232 total genes) and Table 4 showing a 5 differentially expressed gene list (134 total genes). Table 2 has the longest list since it includes the top 15 differentially expressed genes. Table 3 has a gene list that is a subset of Table 2. Likewise, Table 4 has a gene list that is a subset of Table 3. In some instances, a deconvolution matrix comprises at least about 10, 20, 30, 40, 50, 60, 70, 80, 90, 100, 150, 200, or about 250 genes from Table 2. In some instances, a deconvolution matrix comprises no more than about 10, 20, 30, 40, 50, 60, 70, 80, 90, 100, 150, 200, or about 250 genes from Table 2. In some instances, a deconvolution matrix comprises at least about 10, 20, 30, 40, 50, 60, 70, 80, 90, 100, 150, or about 200 genes from Table 3. In some instances, a deconvolution matrix comprises no more than about 10, 20, 30, 40, 50, 60, 70, 80, 90, 100, 150, or about 200 genes from Table 3. In some instances, a deconvolution matrix comprises at least about 10, 20, 30, 40, 50, 60, 70, 80, 90, 100, 110, 120, or about 130 genes from Table 4. In some instances, a deconvolution matrix comprises no more than about 10, 20, 30, 40, 50, 60, 70, 80, 90, 100, 110, 120, or about 130 genes from Table 4.

TABLE 2 Top 15 Differentially Expressed Genes gene_id gene_name gene_id gene_name ENSG00000128203.6 ASPHD2 ENSG00000105369.8 CD79A ENSG00000171777.14 RASGRP4 ENSG00000146373.15 RNF217 ENSG00000186469.7 GNG2 ENSG00000152969.15 JAKMIP1 ENSG00000186806.5 VSIG10L ENSG00000146776.13 ATXN7L1 ENSG00000198894.6 CIPC ENSG00000068831.17 RASGRP2 ENSG00000156475.17 PPP2R2B ENSG00000186891.12 TNFRSF18 ENSG00000178199.12 ZC3H12D ENSG00000155307.16 SAMSN1 ENSG00000206190.10 ATP10A ENSG00000183023.17 SLC8A1 ENSG00000117090.13 SLAMF1 ENSG00000240891.5 PLCXD2 ENSG00000263528.6 IKBKE ENSG00000175857.7 GAPT ENSG00000198851.8 CD3E ENSG00000103313.10 MEFV ENSG00000100351.15 GRAP2 ENSG00000100365.13 NCF4 ENSG00000146285.12 SCML4 ENSG00000164483.15 SAMD3 ENSG00000197208.5 SLC22A4 ENSG00000125810.9 CD93 ENSG00000126217.19 MCF2L ENSG00000178562.16 CD28 ENSG00000186827.9 TNFRSF4 ENSG00000151948.10 GLT1D1 ENSG00000111913.14 FAM65B ENSG00000153563.14 CD8A ENSG00000182183.13 FAM159A ENSG00000134460.14 IL2RA ENSG00000175489.9 LRRC25 ENSG00000132185.15 FCRLA ENSG00000170962.11 PDGFD ENSG00000152582.11 SPEF2 ENSG00000104974.9 LILRA1 ENSG00000101842.12 VSIG1 ENSG00000185883.9 ATP6V0C ENSG00000168229.3 PTGDR ENSG00000151490.12 PTPRO ENSG00000203747.8 FCGR3A ENSG00000157445.13 CACNA2D3 ENSG00000011600.10 TYROBP ENSG00000184060.9 ADAP2 ENSG00000085514.14 PILRA ENSG00000172243.16 CLEC7A ENSG00000104972.13 LILRB1 ENSG00000158869.9 FCER1G ENSG00000065413.15 ANKRD44 ENSG00000100427.14 MLC1 ENSG00000196220.14 SRGAP3 ENSG00000150045.10 KLRF1 ENSG00000162415.6 ZSWIM5 ENSG00000018280.15 SLC11A1 ENSG00000167984.15 NLRC3 ENSG00000122223.11 CD244 ENSG00000178573.6 MAF ENSG00000176928.5 GCNT4 ENSG00000173258.11 ZNF483 ENSG00000162599.14 NFIA ENSG00000187554.10 TLR5 ENSG00000131042.12 LILRB2 ENSG00000069020.17 MAST4 ENSG00000164398.11 ACSL6 ENSG00000181036.12 FCRL6 ENSG00000160683.4 CXCR5 ENSG00000172456.15 FGGY ENSG00000102445.17 KIAA0226L ENSG00000010671.14 BTK ENSG00000160883.9 HK3 ENSG00000114013.14 CD86 ENSG00000198816.5 ZNF358 ENSG00000144218.17 AFF3 ENSG00000179041.3 RRS1 ENSG00000104043.13 ATP8B4 ENSG00000053524.10 MCF2L2 ENSG00000129450.7 SIGLEC9 ENSG00000102245.6 CD40LG ENSG00000082074.14 FYB ENSG00000124203.5 ZNF831 ENSG00000153064.10 BANK1 ENSG00000137441.7 FGFBP2 ENSG00000164867.9 NOS3 ENSG00000109944.9 C11orf63 ENSG00000143226.12 FCGR2A ENSG00000183813.6 CCR4 ENSG00000011590.12 ZBTB32 ENSG00000198879.10 SFMBT2 ENSG00000160185.12 UBASH3A ENSG00000173208.3 ABCD2 ENSG00000163393.11 SLC22A15 ENSG00000144843.10 ADPRH ENSG00000133574.8 GIMAP4 ENSG00000183621.14 ZNF438 ENSG00000196218.10 RYR1 ENSG00000174946.6 GPR171 ENSG00000128218.7 VPREB3 ENSG00000066056.12 TIE1 ENSG00000181847.10 TIGIT ENSG00000176438.11 SYNE3 ENSG00000155849.14 ELMO1 ENSG00000153283.11 CD96 ENSG00000182621.15 PLCB1 ENSG00000167286.8 CD3D ENSG00000148655.13 C10orf11 ENSG00000179934.6 CCR8 ENSG00000128815.16 WDFY4 ENSG00000127507.16 EMR2 ENSG00000188404.7 SELL ENSG00000167850.3 CD300C ENSG00000100368.12 CSF2RB ENSG00000197629.5 MPEG1 ENSG00000141293.14 SKAP1 ENSG00000100385.12 IL2RB ENSG00000213047.10 DENND1B ENSG00000133561.14 GIMAP6 ENSG00000196418.11 ZNF124 ENSG00000179921.13 GPBAR1 ENSG00000113319.10 RASGRF2 ENSG00000263264.1 CTB-133G6.1 ENSG00000140968.9 IRF8 ENSG00000152213.3 ARL11 ENSG00000066294.13 CD84 ENSG00000077420.14 APBB1IP ENSG00000188848.14 BEND4 ENSG00000145416.12 1-Mar ENSG00000183918.13 SH2D1A ENSG00000095585.15 BLNK ENSG00000236609.3 ZNF853 ENSG00000158714.9 SLAMF8 ENSG00000165521.14 EML5 ENSG00000188822.7 CNR2 ENSG00000013725.13 CD6 ENSG00000030419.15 IKZF2 ENSG00000110002.14 VWA5A ENSG00000151366.11 NDUFC2 ENSG00000134539.15 KLRD1 ENSG00000121964.13 GTDC1 ENSG00000170006.10 TMEM154 ENSG00000126264.8 HCST ENSG00000042980.11 ADAM28 ENSG00000010030.12 ETV7 ENSG00000142303.12 ADAMTS10 ENSG00000186265.8 BTLA ENSG00000162881.6 OXER1 ENSG00000187796.12 CARD9 ENSG00000150681.8 RGS18 ENSG00000182866.15 LCK ENSG00000103569.8 AQP9 ENSG00000100450.11 GZMH ENSG00000186074.17 CD300LF ENSG00000158473.6 CD1D ENSG00000172116.20 CD8B ENSG00000149970.13 CNKSR2 ENSG00000100055.19 CYTH4 ENSG00000104490.16 NCALD ENSG00000170909.12 OSCAR ENSG00000107954.9 NEURL1 ENSG00000035720.6 STAP1 ENSG00000155846.15 PPARGC1B ENSG00000139193.3 CD27 ENSG00000003400.13 CASP10 ENSG00000066336.10 SPI1 ENSG00000115956.9 PLEK ENSG00000110448.9 CD5 ENSG00000175556.15 LONRF3 ENSG00000184221.11 OLIG1 ENSG00000187116.12 LILRA5 ENSG00000005471.14 ABCB4 ENSG00000165591.6 FAAH2 ENSG00000105227.13 PRX ENSG00000140090.16 SLC24A4 ENSG00000145990.9 GFOD1 ENSG00000010319.5 SEMA3G ENSG00000159339.12 PADI4 ENSG00000136573.11 BLK ENSG00000105374.8 NKG7 ENSG00000155629.13 PIK3AP1 ENSG00000235568.5 NFAM1 ENSG00000177455.10 CD19 ENSG00000110777.10 POU2AF1 ENSG00000152495.9 CAMK4 ENSG00000154655.13 L3MBTL4 ENSG00000117091.8 CD48 ENSG00000158481.11 CD1C ENSG00000170819.4 BFSP2 ENSG00000140678.15 ITGAX ENSG00000198821.9 CD247 ENSG00000146094.12 DOK3 ENSG00000173762.6 CD7 ENSG00000117009.10 KMO ENSG00000120278.13 PLEKHG1 ENSG00000164124.9 TMEM144 ENSG00000119866.19 BCL11A ENSG00000247077.5 PGAM5 ENSG00000120594.15 PLXDC2 ENSG00000132704.14 FCRL2 ENSG00000145649.7 GZMA ENSG00000107242.16 PIP5K1B ENSG00000158517.12 NCF1 ENSG00000142235.7 LMTK3 ENSG00000180061.8 TMEM150B ENSG00000186854.9 TRABD2A ENSG00000127152.16 BCL11B ENSG00000196159.10 FAT4 ENSG00000116824.4 CD2 ENSG00000106034.16 CPED1 ENSG00000170458.12 CD14 ENSG00000154451.13 GBP5 ENSG00000090376.7 IRAK3 ENSG00000167995.14 BEST1 ENSG00000000938.11 FGR ENSG00000151623.13 NR3C2 ENSG00000143184.4 XCL1 ENSG00000112182.13 BACH2 ENSG00000180739.13 S1PR5 ENSG00000124772.10 CPNE5 ENSG00000012124.13 CD22 ENSG00000221926.10 TRIM16 ENSG00000177272.8 KCNA3 ENSG00000130810.18 PPAN ENSG00000172673.9 THEMIS ENSG00000049768.13 FOXP3 ENSG00000273749.3 CYFIP1 ENSG00000198223.13 CSF2RA ENSG00000278540.3 ACACA ENSG00000271383.5 NBPF19 ENSG00000136404.14 TM6SF1 ENSG00000079263.17 SP140 ENSG00000086730.15 LAT2 ENSG00000073861.2 TBX21 ENSG00000255587.6 RAB44 ENSG00000105383.13 CD33 ENSG00000163519.12 TRAT1 ENSG00000111052.6 LIN7A ENSG00000198734.9 F5 ENSG00000196092.11 PAX5 ENSG00000117322.15 CR2 ENSG00000171051.7 FPR1 ENSG00000065675.13 PRKCQ ENSG00000162654.8 GBP4 ENSG00000198574.5 SH2D1B ENSG00000159958.4 TNFRSF13C ENSG00000187912.10 CLEC17A ENSG00000010610.8 CD4 ENSG00000267534.2 S1PR2 ENSG00000126759.11 CFP ENSG00000119535.16 CSF3R ENSG00000104921.13 FCER2 ENSG00000166523.6 CLEC4E ENSG00000160856.19 FCRL3 ENSG00000164330.15 EBF1 ENSG00000080493.12 SLC4A4 ENSG00000163563.7 MNDA ENSG00000186462.8 NAP1L2 ENSG00000179088.13 C12orf42 ENSG00000261371.4 PECAM1 ENSG00000145687.14 SSBP2 ENSG00000085265.9 FCN1 ENSG00000205544.3 TMEM256 ENSG00000205730.6 ITPRIPL2 ENSG00000172543.6 CTSW ENSG00000266412.4 NCOA4 ENSG00000124406.15 ATP8A1 ENSG00000087903.11 RFX2 ENSG00000136867.9 SLC31A2 ENSG00000161405.15 IKZF3 ENSG00000113263.11 ITK ENSG00000144152.11 FBLN7 ENSG00000172578.10 KLHL6 ENSG00000165071.13 TMEM71 ENSG00000119457.7 SLC46A2 ENSG00000265808.3 SEC22B ENSG00000153485.5 TMEM251 ENSG00000162804.12 SNED1 ENSG00000203710.9 CR1 ENSG00000105967.14 TFEC ENSG00000175294.5 CATSPER1 ENSG00000197540.6 GZMM ENSG00000111452.11 GPR133 ENSG00000090612.19 ZNF268 ENSG00000160654.8 CD3G ENSG00000171596.6 NMUR1 ENSG00000189430.11 NCR1 ENSG00000197705.8 KLHL14 ENSG00000089012.13 SIRPG ENSG00000181409.10 AATK ENSG00000112394.15 SLC16A10

Provided herein are systems and methods for determining an immune-oncology profile comprising determining cell type and ratio using deconvolution methods, wherein following deconvolution, percentages of immune cells may be determined. In some instances, immune cells may be further grouped based on shared lineage and percentages of immune cells based on lineage is determined. For example, immune cells are divided into T cells, CD4+ subtypes, myeloid cells, and natural killer cells. In some instances, percentages of non-immune cells are determined. In some instances, percentages of immune cells and percentages of non-immune cells are determined. Sometimes, an immune-oncology profile comprises determining a percentage of immune cells and non-immune cells such as tumor cells and/or stromal cells.

Following deconvolution, a number of cell types of various immune and non-immune cell types may be determined. In some instances, deconvolution identifies at least or about 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, or more than 20 immune cell types. In some instances, deconvolution identifies a range of about 5 to about 20 immune cell types. In some instances, deconvolution identifies at least or about 5 to 10, 5 to 15, 5 to 20, 10 to 15, 10 to 20, or 15 to 20 immune cell types. Deconvolution may be used to identify non-immune cell types. In some instances, deconvolution identifies at least or about 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, or more than 20 non-immune cell types. In some instances, deconvolution identifies a range of about 5 to about 20 non-immune cell types. In some instances, deconvolution identifies at least or about 5 to 10, 5 to 15, 5 to 20, 10 to 15, 10 to 20, or 15 to 20 non-immune cell types. In some cases, deconvolution results are evaluated by comparing to the Gold Standard. Sometimes, the Gold Standard is generated by sorting the samples evaluated by deconvolution. For example, a sample is split into two portions with one portion evaluated by nucleic acid sequencing and deconvolution and the other portion evaluated by sorting (e.g., flow cytometry or FACS) to obtain the Gold Standard. The results of the deconvolution are then compared to the Gold Standard to evaluate for accuracy, specificity, sensitivity, correlation to the Gold Standard, or any combination thereof.

Provided herein are systems and methods for generating an immune-oncology profile comprising mutational burden determined using sequencing data. In some instances, mutational burden is calculated for somatic mutations. In some instances, mutational burden is calculated by excluding germline variations. Germline variations may be excluded based on frequency. In some instances, exclusion is based on a frequency of at least 0.01%, 0.05%, 0.1%, 0.5%, 1%, 2%, 5%, 10%, 15%, 20%, 25% or more than 25%. In some instances, the germline variations are determined using germline variation databases.

Mutational burden may be determined using a plurality of genes. Examples of genes used to determine mutational burden are seen in Table 5. In some instances, a number of genes for determining mutational burden is at least or about 250 to 5,000 genes. In some instances, a number of genes for determining mutational burden is at least or about 250 genes. In some instances, a number of genes for determining mutational burden is at most 5,000 genes. In some instances, a number of genes for determining mutational burden is at least or about 250 to 500, 250 to 750, 250 to 1,000, 250 to 1,500, 250 to 2,000, 250 to 2,500, 250 to 3,000, 250 to 3,500, 250 to 4,000, 250 to 4,500, 250 to 5,000, 500 to 750, 500 to 1,000, 500 to 1,500, 500 to 2,000, 500 to 2,500, 500 to 3,000, 500 to 3,500, 500 to 4,000, 500 to 4,500, 500 to 5,000, 750 to 1,000, 750 to 1,500, 750 to 2,000, 750 to 2,500, 750 to 3,000, 750 to 3,500, 750 to 4,000, 750 to 4,500, 750 to 5,000, 1,000 to 1,500, 1,000 to 2,000, 1,000 to 2,500, 1,000 to 3,000, 1,000 to 3,500, 1,000 to 4,000, 1,000 to 4,500, 1,000 to 5,000, 1,500 to 2,000, 1,500 to 2,500, 1,500 to 3,000, 1,500 to 3,500, 1,500 to 4,000, 1,500 to 4,500, 1,500 to 5,000, 2,000 to 2,500, 2,000 to 3,000, 2,000 to 3,500, 2,000 to 4,000, 2,000 to 4,500, 2,000 to 5,000, 2,500 to 3,000, 2,500 to 3,500, 2,500 to 4,000, 2,500 to 4,500, 2,500 to 5,000, 3,000 to 3,500, 3,000 to 4,000, 3,000 to 4,500, 3,000 to 5,000, 3,500 to 4,000, 3,500 to 4,500, 3,500 to 5,000, 4,000 to 4,500, 4,000 to 5,000, or 4,500 to 5,000 genes.

Mutational burden as determined herein may be determined as a range between low and high mutational burden. In some instances, mutational burden is determined as low, medium, or high mutational burden. Sometimes, mutational burden is determined as the number of nonsynonymous somatic mutations per megabase in the exome. In some cases, mutational burden is compared to the Gold Standard mutational burden calculated using paired normal analysis of DNA. Specifically, the Gold Standard mutational burden measures somatic mutations using DNA sequence data obtained from the sample by comparing allele frequencies in normal and tumor sample alignments, annotating the identified mutations, and aggregating the mutations.

TABLE 5 Mutational Burden Genes TC2N TRAF6 PRMT2 STIM2 DDX59 EYA3 DPF2 LIPA TRAF5 PRMT3 STIM1 DDX58 AGAP3 UBQLN4 TBL3 GDPD5 PRMT6 N4BP1 DDX54 AGAP6 UBR1 LIMA1 GEM SMARCA2 N4BP2 ATP6V0A2 AEBP1 ARID1B LIN54 GKAP1 SMAP1 N4BP2L2 DDX51 ADSS ARRDC1 LIMK1 TPRKB SMAD7 NDUFA3 DDX50 ADPRH ARRB2 TCF4 TPR PRKRIP1 NHLRC2 DDX5 FADS1 UBR2 TCF3 TPP2 SMARCC2 NHLRC3 ZNF438 TUBG1 DNAJB14 LIN7B TPP1 PRKAG2 NID1 ATP5SL ADNP DPH1 TCF25 TPMT SMARCC1 NID2 DENND2D ADNP2 DPH2 TCF20 GLA PRKAR1A NGDN DENND1A TUBGCP2 DPP7 TCF12 GLCE PRKAR1B NIN ATP5G2 ADSL ARID2 TCERG1 GIT2 PRKAR2A NIPAL2 UPF3B FAAH DPP3 TBL1X GIPC1 PRKCA STAB1 UQCC2 ZNF707 ARID4A TBKBP1 GIGYF2 PRKCD STAG1 UQCRB F8 ARID4B LMO7 GIMAP4 PRKCE NDUFA4 BMI1 F3 ARID5B LMTK2 GIMAP6 SMARCB1 NFKBIE USP35 ADRM1 ARRDC3 TBK1 GIMAP7 PRKCI NFIX USP38 EVI2B EFNB1 LNX2 GOLGA5 PRKCZ NFKBIA ZNF384 AGFG1 ANO10 LONP1 TP53 SMAD4 NFYC USP40 AGRN EFTUD2 TBC1D8 TOX4 SMAD3 NFRKB BET1 AGTPBP1 DHX34 LOXL1 TNKS SLMAP NFX1 BFAR ZNF691 ZNF574 TBC1D5 TNK2 PRR14 NFYA USP47 EXOC2 DHX32 LMNB1 TNIP1 PRR14L NIPBL ZNF37A EXOC1 DHX36 TBCK GRK5 SLTM NIPSNAP1 USP34 ZNF689 DHX37 TBCEL TNFRSF21 SLPI NLRX1 BDH1 AHCTF1 ANP32B TBCE TNFRSF1B PROSER1 NMD3 BHLHE40 EXD3 DHX57 LLGL2 TNKS1BP1 PRR4 NISCH USP24 EXD2 ATG16L2 LLPH GRB10 PRRC2B NME6 CYP51A1 TUT1 DHX30 TBCD GPS2 PRR12 NME7 ZNF397 AHCYL1 EHMT1 LMAN2L TNPO2 PRPSAP2 NLRP1 BCL2L11 AHCYL2 EHHADH LMBRD1 GPRC5C SMAD2 NLRC5 BCL2L12 AHDC1 ZNF576 LMBRD2 TNKS2 PRPF18 NLN BCL2L13 AHI1 ANKS1A LMF1 GRAMD1A PRPF3 ST7L BCL2L2 AHNAK EHD1 LIMD1 GRN PRPF38B NKAP BCL6 AHR EHBP1L1 TCF7 GSTO1 PRPF4 NKTR BCL7B EVL EHBP1 TECPR1 GTDC1 PRPF40A ST6GALNAC4 USP25 EVI5L EGR2 LCMT2 GTF2E2 PRPF8 ST3GAL4 USP28 EVI5 EGR1 TECR GRWD1 SMAD1 NFIA BCL9 AGPS ZNF568 LCOR GSAP PPP4C NFE2L1 BCL9L EXT2 EFCAB2 LCORL TNFRSF10B PPP4R1 NDUFB8 BCLAF1 AGFG2 DIEXF LCP1 GSPT1 SMG6 NDUFB9 USP3 EXT1 ANXA6 LDB1 GSPT2 PPP6C NDUFC2 BCOR AGGF1 ATF7IP2 LDHA GSR PPP6R1 NDUFS2 USP30 AGK AOAH LDLR TNRC18 PPP6R3 NDUFS7 BCR AGL UBE2E2 LDLRAD4 TNRC6A PPRC1 NDUFV1 USP31 AGO1 DIP2A TDRKH TNRC6B PPWD1 NECAP1 USP32 EXOSC7 DIP2B LCLAT1 GOSR1 SMG7 NDUFA8 USP48 AGO2 ATF6 TELO2 GOSR2 PPP1R7 NDUFA9 CYP20A1 EXOSC2 ATF5 LATS1 TOPBP1 PPP2R5A STAM BLMH EXOSC10 ATF4 TET2 TOP3B PPP2R5B NEO1 CYB561A3 AGO4 DIDO1 LBR TOP2B PPP2R5C NEU3 CYB561 EXOG DHX8 TESK2 GPALPP1 PPP2R5E NEURL4 USPL1 EXOC7 DIAPH1 TESK1 GPAM PQLC1 STAMBP CXorf40A EPS8L2 ANTXR2 TESC GPATCH2 PQLC3 NEDD1 BLZF1 ZNF615 ANXA1 TERF1 GPATCH2L PRKAA1 NF1 BIVM EML4 ZNF571 TEP1 GOPC PREPL NFATC1 USP5 EML3 ANXA2 TDRD7 TOR2A PRDX5 NFATC2IP ZNF362 UBA7 ANXA3 TCP11L2 TOR1AIP1 PRDX6 NFATC3 USP53 ANKAR DICER1 TCP11L1 TOPORS PREB NENF USP54 ANKDD1A EFCAB7 TCOF1 GOLGB1 SMG1 NEDD9 ZNF358 ZNF609 ATG2A LHPP GOLIM4 SMARCD1 NEK1 USP6NL ZNF608 EIF4A2 TCHP GOLM1 PRIMPOL NEK3 USP7 ANKHD1 EIF3G LIG3 GON4L PRADC1 NEK4 CYLD ANKIB1 ATG9A LGALSL GPATCH8 SMCHD1 NEK6 BIN1 ZNF606 ANKRD36 LGALS9 TNRC6C SMC4 NEK7 USP9X UBA3 DHRS3 LEPR GPR155 PRC1 SPATA7 CYHR1 ANAPC1 ANKRD39 LETMD1 TOM1L2 PRCC PLEKHA5 CYFIP2 ENOSF1 DHRS12 TDP2 GPBP1 PRDM10 PLEKHB2 CYCS UAP1 EIF4G3 LFNG TNS3 PRDM11 PLEKHG1 CYBRD1 ENO1 EIF4G2 TDP1 TNS1 PRDM15 PLEKHG2 CYBB ANAPC7 DHCR7 TDG GPR137 PRDM2 PLEC BIRC3 ENKD1 EIF4G1 LGALS3BP TOP1MT PRDM4 SNIP1 BIRC6 ENGASE UNK TCTN3 GPD2 PRRC2C PLEKHJ1 CYB5R4 ENG ATHL1 TCTN2 TOP1 QKI PLEKHM2 B3GNTL1 ANAPC2 ZNF592 TBC1D4 GPR107 PTPRE PLEKHM3 DBN1 ANKLE2 ATG7 LTA4H GPR108 PTPN18 PLEK DBF4B ANKRD13C ATG4B LTBP1 FLYWCH1 PTPN2 PLCD1 DBF4 ELK4 EIF2AK3 LTBP3 FMNL1 PTPN23 PLAGL2 DAZAP1 ELK3 ANKRD50 LTBR FMO5 PTPN6 PLAUR USP12 ANKRD16 EIF2AK2 LTN1 FMR1 PTPRA PLBD1 USP13 ANKRD17 ATG4A LTV1 FN1 PTPRC PLCB2 USP14 UBAP1 ANKRD42 LUM FLNA PTPRF PLCB3 USP15 ZNF597 ATG2B LUZP1 FNBP4 PTPRJ SNRK BACE2 ELF1 DHTKD1 TAMM41 FNDC3A PTPRM PLCG1 BACH1 UBAP2 DHX15 LSG1 FNDC3B PTPRS PLCL2 B4GALT2 UBAP2L EIF2AK4 TAOK2 FLNB PTRHD1 SNRNP200 DCAF4 ANKRD26 ANKRD44 TAOK1 FKBP7 SLFN13 PLD2 DCAF17 ANKRD27 ZNF585A TANGO6 FKBP15 PTEN PML DCAF16 ELAVL1 EIF3E TANGO2 FKBP1C PTGES2 PLXNB1 DCAF13 EIF5B EIF3D LRSAM1 FKBP2 PTK7 PLXNB2 BAG3 ANKRD28 ANKRD46 LRWD1 FKBP4 PTOV1 PLXND1 BBS2 ANKRD12 EIF3C LSM6 FKBP5 PXMP2 SNAPC4 DAB2 ELL2 ATG4D LSM4 FKBP8 PXN PMPCA BBS9 ANKRA2 EIF2S3L LYSMD4 FLCN SLC4A7 PMPCB DAAM2 ANKMY1 DHRS4 LYST FLI1 PYGB PMS1 CYYR1 EMC10 EIF2D TAF2 FNIP1 PYGL PMS2 CYTIP EMB EIF2B3 TAF1C FNIP2 PYGO2 PLXNA3 CYTH4 ELP6 DNAJC24 LZTR1 FNTA PYROXD2 PLXDC2 CYTH3 ELP4 E4F1 LZTS2 TRMT10A QARS PLXDC1 BCAS3 ANKMY2 ATAD3B MACF1 FOXN2 PXK PLK3 CYTH1 ELOVL5 DLAT LYAR FOXO4 PXDN SND1 USP21 ELL3 APEX2 TAF3 FOXP1 PWWP2B PLOD1 BCCIP ANKRD10 DLG5 LYPLAL1 TRIP6 PUM1 PLOD2 BCKDHA ELOF1 EDC3 LRRK2 TRIP4 PUM2 SNAPIN BCKDHB ELMSAN1 AP3B1 LRRK1 FOXJ2 PURB PLRG1 USP20 ELMO2 EDF1 LRPAP1 TRNAU1AP PUS7 PLAC9 BAG4 ELMO1 EDEM3 LRP1 TRMU PUS7L PIK3R4 BBS1 ZNF619 ULK3 LRP12 FOSB PWP1 PIK3R5 BAG5 ATL3 EDEM2 TBC1D22B FOSL2 PWP2 PIKFYVE DAPK1 ENOX2 APIP TBC1D22A TRMT6 PTDSS1 PIM2 BANP ALDH5A1 UBE2I LRP5 TRMT5 SLC7A6 PISD BAP1 ALDH9A1 ATAD2B LRPPRC TRMT2B PSMA2 PIN4 USP19 TYW1 ECHDC2 LRRC14 FDPS PSMA4 PINX1 ZNF408 ALG11 APAF1 TBC1D15 FCGR3A PSMB5 PIP5K1A ZNF407 ALG12 APBA3 LRMP FCHO2 PSMB7 PIK3R1 BASP1 ALG13 ECH1 TBC1D23 FCHSD2 SLC8B1 PIK3CB DAGLB ALG14 ATAD2 TBC1D24 TSHZ1 SLC9A1 PIGO BAZ1A ALG3 APBB1IP LRIG2 FES PRSS23 PIGQ BAZ1B ALG6 APBB2 LPCAT2 FDXR SLFN11 PIGT BAZ2A TYW5 DLG1 LPCAT4 FECH SLCO3A1 PIGX DAG1 EPG5 APC LPIN1 FCGR2A SLCO2B1 SNW1 BAZ2B EPDR1 ATAD1 LPIN2 FCER1G SLC9B2 PIH1D1 CEP95 EPC2 ECI1 LPP FBXO6 SLC9A8 PIK3C2A CEP85L ALG8 AP4B1 LPXN FBXO8 PRUNE2 PIK3C2B CEP78 EPC1 DLD LRBA FBXW11 SLC9A3R1 PIK3C3 CEP70 ALDH4A1 ZNF565 LRCH1 FBXW9 PSD4 PIK3CA CEP57L1 EPHB4 DLG4 LRCH3 TRPM7 PSEN2 PKM CEP57 AKT3 ECD LRCH4 FGFRL1 PSTPIP1 PKN1 CEP41 EPS15L1 ECE1 TBC1D2B FGGY PSMF1 PKNOX1 CEP350 EPRS DLG3 LRIF1 TRPT1 PSMG1 PKP4 WWP2 TYK2 UMPS LRRC28 FGR PSMG4 PLA2G4A CEP250 ZNF668 APMAP TARSL2 FHL2 PSPC1 PLA2G6 CEP192 EPOR AP1B1 TARS2 FHOD1 PSPH PITPNB CEP170 EPN2 EEF1G TARDBP FICD PTBP1 PITPNC1 CEP135 EPHB6 EEF1A1 TARBP1 FIG4 PTBP2 PITPNM1 CBWD3 ALCAM EEF2K TAPT1 FIP1L1 PTCD1 SNTB1 CEP89 ALDH16A1 DIS3L2 LRRC8A FGFR1 PTCD3 SNRPN CBFA2T2 EPN1 AP1M1 LRRC8B TRRAP PTCH1 PKD1 CBL EPM2A DZIP3 LRRCC1 FEZ2 PSME4 PKDCC CBLB ALDH1A1 EEF1D LRRFIP1 FGD2 PSME2 PNISR CBLL1 ALKBH1 EEF2 LRRFIP2 FGD3 PSMC6 PPAN WWC3 U2SURP UNC45A LRRC61 FGD6 PSMD12 PPARA CES4A ZNF638 DIRC2 LRRC32 TSC22D1 PSMD3 PPARG ZBTB5 ENTPD6 ZNF559 LRRC37B TSC2 PSMD5 PPFIA1 CES2 ALS2 UNC13D TBC1D10B TSC1 RIC8A PPFIBP1 CES1 ENTPD1 ULK1 TBC1D10A FPGT SAV1 PPFIBP2 CERS6 ZNF627 AP2M1 TBC1D1 GALM SART1 PPIA WWOX AMBRA1 ULK2 TAX1BP1 GALNS SATB1 POU6F1 WWP1 ZNF626 DIS3 TATDN2 GALNT10 SHOC2 SMPD4 WRNIP1 AMFR ASUN LARS2 GALNT2 SBF1 POP4 XAF1 ZNF623 EED TIMELESS GALT SBF2 POR ZBTB43 ENPP4 AP2A2 KHNYN GANAB SHKBP1 SMOX CCDC146 AMN1 EEA1 KHSRP GANC SBNO1 POU2F1 XIAP AMPD2 DLGAP4 KIAA0100 TRIP12 SAFB PPP1CC CECR5 AMPD3 AP1AR KIAA0141 TRIM22 SAFB2 PPP1R12A CCDC149 ENTPD7 CCDC68 KIAA0196 TRIM16 SHPRH PPP1R13B CECR1 ALKBH3 ASS1 KDM6B TRIM14 SAMD9L PPP1R15A ZBTB40 EP400NL ZNF813 KDM5C TRIM11 SAMHD1 PPP1CB ZBTB4 ALKBH4 ZSCAN12 KIF3A GAK SAMM50 PPIL2 ZBTB39 ALKBH5 PRICKLE3 KCTD9 TRAPPC9 SAP130 PPIP5K1 ZBTB38 EPB41L3 ZNF471 KDM1A TRAPPC3 SBNO2 PPIP5K2 CEP104 EPB41L2 NOSTRIN KDM2A GAPVD1 SH3RF1 PPM1B CBX5 ZNF655 A4GALT KDM5B GCC1 SCMH1 PPM1L CBX6 ALMS1 ZRANB3 KDM2B GBP2 SCML1 PPM1M CENPQ EPB41 PPP1R26 KDM3B TRAPPC12 SH3TC1 POMT2 CBX7 EPAS1 ABHD6 KDM4A TRAPPC10 SCN1B POMT1 CBY1 ALOX5 CBS KDM4B GCAT SH3RF3 POMP CC2D1A EP400 CD248 KDM4C GCC2 SCAF1 POGZ CC2D1B EP300 NFASC KDM5A TRAP1 SH3KBP1 POLA1 ZBTB48 ALOX5AP SEMA5A KIAA0232 TRANK1 SCO1 POLD1 CCAR1 EOGT CD300A KIAA0355 GBF1 SCP2 POLK CCAR2 ALPK1 ABI3BP TIE1 GBE1 SCPEP1 POLE CENPC ZNF641 NES KIAA1715 GART SHB POLH CCDC109B FADS2 CD2 KIDINS220 GAS2L1 SCAF4 POC5 CCDC115 FADS3 NOTCH3 KIF13A GAS6 SCAF8 SMYD3 XAB2 AC138035.2 STAG3 KIF13B GATAD2A SCAP POC1B WSB1 AC009403.2 SLC7A5 KIAA0368 GATAD2B SCAPER SNAP29 WRN ZRANB2 ACSM3 KIF1B GATM SCARB2 SMYD5 CAPS AC013461.1 ZAP70 KIF1C GBA SCD PNPLA6 CHKA ZNFX1 PTPRU KIF22 TRIM24 SCFD2 PNPLA8 CHID1 ZNF91 ABLIM3 TICAM1 FTSJ3 SAAL1 POLI WHSC1L1 FAM73B CCDC80 TIAM2 TRIM5 S1PR3 POLL ZC3HAV1 FAM73A SEMA3C TIAM1 TRIM44 RSBN1L POLR2M CAPZA2 ZNF880 SEMA4A KIAA1586 FTO RSF1 POLR3A ZC3H7B ZNF862 AC005943.2 KIAA1551 FUBP1 SIK3 POLR3B CARD16 ZSCAN21 PPP1R13L KIAA1468 FUK SIK1 POLR3C CHFR ABLIM1 SGCE KIAA0391 FURIN RSPRY1 POLR3D ZC3H7A FANCC ABI3 KIAA0430 TRIM52 RRP9 POLR3E ZC3H6 ABI2 NFIB KIAA0556 TRIM56 RRP8 POLM CHD9 ABL1 NCKAP1L KIAA0586 FRA10AC1 RRP36 POLRMT CHD8 FANCA SEMA6D KIAA0753 TRIP11 RRBP1 POM121 CHD7 FAN1 SFRP1 KIAA0922 FRG1 RREB1 SMURF1 CHD6 TSPAN7 SASH1 KIAA1109 TRIOBP RRM2B SMU1 CARD6 ABL2 PPP1R16B KIAA1191 FRMD4B RRP1B SMTN CHD4 FAM98C SASH3 KIAA1324L TRIO S1PR1 SMYD2 CHD3 FAM98B PTPRG KIAA1328 FRY RXRA POLR1B CHD1L FAM98A NCEH1 KAT6B FRYL RYBP POLR2A CHM ZSCAN25 SH3BP4 KANSL2 TRIM68 SIGIRR POLR2B CAPRIN2 ABR PTPRB KANSL3 FUS S100A10 POLR2E CAND1 ZSCAN30 AXL KAT2B TRIM34 SIAH2 POLR2F CHMP4B FAM84B PTN KAT6A GAA S100A8 POLR2G CAPG ABRACL SLC9A3R2 KAT7 TRIM41 RTEL1 PCF11 ZCCHC11 ABT1 ACE KBTBD6 G3BP1 RTF1 SOS1 CAPN15 ABTB1 SH3PXD2B KAT8 G2E3 RTN3 SORT1 CAPN3 TSR1 NMNAT3 KATNB1 FUT8 RTTN SORL1 CAPN5 ZNF844 PRDM1 KATNBL1 FYB RUFY1 SORBS3 CAPN7 ACER3 PTAFR KBTBD3 FYCO1 RUFY2 SORBS1 ZC3HC1 ACADVL CCDC122 KANSL1 FYN RUNDC1 SON CHML FAM47E PSTPIP2 KANK2 FZD1 RUSC1 PCGF5 CARD8 TTBK2 ZNF441 JMJD6 GTF2IRD2B RUSC2 PCIF1 CASP10 ZNF841 CCDC121 TM9SF4 TMEM173 RUVBL1 SOS2 ZC3H13 TTC13 NEDD4 JUNB TMEM168 RUVBL2 SOCS2 WLS ACAP1 B3GALNT1 JUND TMEM167B SCRIB PBRM1 CFLAR ACAP2 ZBTB45 JUP IGHMBP2 SGPL1 PBXIP1 CFL2 ACAP3 ATP8B4 KANK1 IGF2R SGTA PC CFL1 FAM46A SERAC1 KBTBD7 TMEM165 SGSM2 PCBP2 CASP4 ACAT1 ZNF429 TIMM50 TMEM161A SGSH SP1 WNK1 ACAT2 NINL TIMP1 TMEM175 SERPINB6 PCCA CASP6 ACBD3 CCND1 KCTD10 TMEM176A SERPINB8 PCCB CASP9 ACBD4 SLC9A9 KCMF1 ILVBL SGPP1 PCDH1 ZC3H11A ACBD5 SERINC2 KCTD13 IFRD2 SERPING1 SP2 ZC3H10 FAM35A ATXN7L2 KCTD18 IFT122 SERPINH1 SP140L CAST TTC17 PTGER4 KCNAB2 IFT140 SERPINI1 SP110 CAT ACCS SERPINA3 TLR4 IFT172 SERTAD1 SP100 CATSPER2 ACD PRKD1 TLR1 TMEM176B SESN1 PDCD6IP ZBTB7B FAM49A ZNF431 TLN1 IFT88 SEPT2 SOCS5 WRAP73 ACAD11 ASAP3 TLK2 IGF1R SEPT5 PDE2A WIZ AC138969.4 PTGFRN TLK1 IKBKAP SEPT7 PDE4DIP ZC3H14 TSSC1 AVIL TLE4 IKZF1 SEPT9 PDE5A CARF TSSC4 PTGR2 TLE3 TMEM131 SH2D3C PDE7A CARHSP1 ACAA1 PTGS1 TJP2 IL2RG SERINC3 PDE8A WIPF2 ACAA2 ABCC9 KRT8 IL32 SERPINA1 PDGFC CHAMP1 TST PPP4R1L TFPI IL4R SF3B4 PCNT CHAF1A TSTA3 SMARCA1 TFEB ILF3 SFI1 PCOLCE2 ZC3H4 ACACB SHC2 TFDP1 IL1R1 SFMBT1 PCSK7 CARS ACAD10 ABCA6 TFCP2 IL10RA SFPQ PCYT1A CARS2 FAM65B PROCR TFAP4 IL13RA1 SFSWAP SOCS6 ZC3H3 ACAD8 CC2D2A TIA1 IL15RA SFT2D2 PDCD11 ZC3H18 ACAD9 SLIT2 KPNA3 IL16 SET PAXIP1 ZC3H15 ACADM SCUBE2 KPNA4 IL17RA SGK3 PAXBP1 CASC4 TSTD1 PROS1 TGIF2 IL17RC SGK1 PAFAH1B2 CASK FAM53C SGK494 KPTN TMEM144 SFXN2 SPATA13 ZBTB34 ACADS SCARA3 KRCC1 IFNGR2 SFXN5 PAN2 CHMP7 ACADSB AASS TGIF1 IFNGR1 SF3B3 PAK2 CDC34 TSTD2 SLIT3 KRIT1 IARS SF3B2 SPAG9 CDC27 ABI1 PPP1R3D TGFBRAP1 HUWE1 SF3B1 PALB2 YBX1 ABHD8 PPP1R3C KRT10 HYOU1 SF3A3 PAM CCNK ABHD5 SEPT10 TGFBR3 IARS2 SETD1A P4HA1 CDC25B ABHD4 ACOX2 KSR1 IBA57 SETD1B P4HA2 CCP110 AARS SLC8A1 KTN1 ICA1 SETD2 PABPC1L CDAN1 AARS2 ZNF827 LARP1 TMEM184B SETD3 PACS1 CDC40 AARSD1 ABCA7 LARP7 HTT SETD5 PACSIN2 CDCA7L FBXL20 SHF LAMC1 HTRA2 SETD6 PAN3 YTHDF2 AASDH ATP8B1 TEX10 HSPG2 SETD7 PARP12 YTHDC2 AASDHPPT CCR1 LAMB2 HTATSF1 SETDB1 PARP14 CDC5L ABAT ZNF845 LAMB1 TMEM206 SETDB2 PARP3 CCNB1 ABCA1 PSD3 L2HGDH TMEM2 SETX PARP4 CDC42EP4 ABCA2 ZNF852 L3MBTL2 TMEM192 SGMS1 PARP6 CDC42EP3 ABCA5 ZNF443 LACTB IFNAR2 SF3A1 PARP8 CCND2 FBXL19 SETBP1 LAIR1 IFIH1 SF3A2 PARVB CDC42BPB ABCB1 SLC7A2 TEX2 IFI27L1 SH3BGRL2 PARVG CDC42BPA ABCB10 ZBTB46 LAMA5 IFI30 SDPR SPAG16 CD99L2 FBXL14 SCD5 KPNA1 IFIT2 SH3BP5L PASK CD55 FBXL12 STARD8 KNTC1 IFITM3 SEC11A PATL1 CCZ1B FBRS STARD13 KLHDC3 IFNAR1 SEC14L1 PAWR CD47 ZW10 CCDC3 KLF6 IDS SEC24B PARP10 CD44 ABCB6 CCDC102B KLF7 HSPBAP1 SH3BP5 PANK4 CD14 ABCB7 NDN KLF9 TMCO3 SH3BP2 PAPD5 CD40 ABCB8 SH3D19 KLHL18 ISOC1 SEC16A PAPLN CD4 FBXL6 ABCA8 THOC5 TMCC3 SEC23A PAPOLG CD163 FBXO25 SPAG1 THOC2 ISY1 SEC23B PAPSS2 YIPF3 A2M BTNL9 KIF9 ITFG1 SEC23IP PARL CD36 FBXO38 PARVA KIFAP3 ITFG2 SCYL1 PHC1 YIF1A ZZEF1 ALDH7A1 KIFC2 ITGA5 SDAD1 PHC2 CD302 AAAS PARD3B THUMPD3 ITGA7 SDCBP PHF10 CD2AP FBXO28 PARD3 KLC1 ITGAE SDCCAG8 PHF12 YES1 AACS RBM47 KLC2 ITGAL SEC24C PHB CD93 ZYX C3 KLC4 ITGAM SEMA3F PHF2 CD9 TSPAN14 C3AR1 THRAP3 TMCO4 SEMA6A PHF20 YLPM1 ZXDB ROBO1 KLHL2 IRF2BPL SEMA6C PHF20L1 CD86 FBXO22 C3orf33 KNSTRN IRF3 SENP1 PHF23 CD83 FBXO18 PIK3AP1 TGS1 IRF8 SEC24D SNX14 CD82 AAED1 PID1 THAP4 TMED4 SENP5 PGM1 YBX3 FBXO11 PCDHGC3 THADA TMED1 SENP7 PGD CD74 AAGAB ZNF283 KMT2A ISG15 SEPP1 PGGT1B CCSER2 AAK1 SORBS2 KMT2C ITGAX SEC31A SNX17 CCT2 AAMDC SLC38A5 KMT2D ITGB1 SEC31B PGRMC2 CCT3 AAMP C10orf128 KMT2E JAG1 SEC61G PHACTR2 CCT4 ZXDC ZNF14 TGOLN2 IWS1 SECISBP2 PHF3 CD63 AAR2 SOX13 THBD JAK2 SEL1L3 PI4K2A YIPF6 ABCC1 SOX7 KLHL21 TMA16 RIC8B PI4KA ZBTB14 TSPAN3 RBP1 KLHL22 JARID2 RNF8 PIAS4 CDKN2AIPNL FBN1 ZNF135 THEM4 IVD RNGTT PICALM CDKN2AIP FASN PBLD KLHL5 ITSN2 RNH1 PICK1 CCDC28A FARSB SLC39A14 KLHL7 ITSN1 RNMT PIGC XPR1 ABHD13 PALMD THBS1 ITGB2 RNPC3 PIGG XRCC1 FARSA NPAS2 MAD1L1 ITGB4 ROBO3 PHYKPL ZBTB11 ABHD14A SLC25A23 MRPL1 ITIH4 ROCK2 PHYHD1 CDKAL1 FARS2 ZNF555 STYXL1 ITM2A SLC25A39 PHYH CDK8 ZSCAN31 RASAL2 MRPL10 ITPKB RNF214 PHGDH ZBTB10 ABHD14B P2RX7 SUCLG2 ITPR1 RNF217 SNX13 ZBTB1 ABHD11 ZNF554 MPP5 ITPR2 RNF34 PHIP CDK5RAP3 ABHD15 RARRES2 MPP6 ITPRIP RNF38 PHKA2 CDK5RAP2 ABHD16A SPDYE3 MPP7 IRF2 RNF4 PHKB CDK5RAP1 ABHD17A RARG SUCO INPP5A RNF40 PHLDB2 CCDC22 ABHD17B OTUD3 MPST INO80 RP11- PHLPP1 CCDC57 ABHD17C PLCB1 231C14.4 MPZL1 INO80C RP11- PHLPP2 ZBTB25 ABHD18 SLC22A17 166B2.1 MR1 INO80D SLC24A1 PHOSPHO2 ZBTB24 ABHD2 SLC1A3 MRAS INPP5B SLC22A23 PHRF1 XPNPEP1 ABHD3 PALLD MRC2 INPP5D SLC22A18 PGBD2 ZBTB21 ABHD12 PALD1 MRE11A INPPL1 SLC25A36 PGAP3 XPO1 ABHD10 APCDD1 MRPL54 TMEM109 SLC1A5 PDXDC1 XPO5 ABCC10 ZNF322 MRPL33 IMP4 SLC25A13 PDZD8 XPO6 ABCD4 SPARCL1 MRPL35 IMPA2 SLC25A14 PEAK1 XPO7 FBLN5 SLC25A33 MRPL38 IMPACT SLC25A32 PEAR1 ZBTB17 ZSWIM8 PKN3 MRPL39 INCENP SLC25A26 PEBP1 CDR2 ZSWIM6 RBFOX2 MPHOSPH6 INF2 SLC25A16 PECR ZBTB16 ABCC3 RAVER2 MLLT3 ING3 RNF213 PELP1 CCDC71 ABCC5 RCAN2 MLLT4 ING4 RLF PDS5B CCDC88B ABCD1 AOC3 SUN1 IPO8 RLIM PDS5A CCDC88C ABCD3 PGM5 MLXIP IPO9 SLC29A3 PDIA4 CCDC9 ZSCAN9 ZNF248 MMAA IQCB1 RMDN3 PDIK1L CCDC91 ABCE1 RHBDF1 MLLT1 IQCE RMI1 PDK4 CCDC92 ABCF1 ZNF205 MMD IQCG SLC29A1 PDLIM5 CCDC93 ABCF2 PHACTR1 SUMO3 IQCK SLC27A4 PDPR CCDC94 ABCF3 C1orf112 SUMF2 IQGAP1 SLC2A11 PEMT CCDC97 ABCG1 PDGFRB SUMF1 IQGAP2 RICTOR PER1 XRN1 FASTKD3 ANK3 SUPT20H IQSEC1 RIF1 SNX3 CDK4 FASTKD2 PDGFRA MKL1 IRAK1 RIMKLB PFKFB2 CCDC69 ZSWIM4 ZNF582 MKL2 IREB2 SLC2A3 PFKFB3 CDK2AP2 FASTKD1 PDE9A MKLN1 IPO7 RIN2 PFKP CCDC61 ZSWIM1 RGS5 MKS1 IPO5 RIN3 PER2 CDK19 TTC21B RFX3 SUOX IPO4 RIOK1 SNX29 CDK18 TUBA1B ZNF570 SUN2 IPO13 RNF2 SNX25 CDK14 ADAR RGL1 MLF1 INSR SLC26A2 PFAS ZBED5 ADARB1 RGL3 MLH1 INTS1 SLC26A11 SNX30 CDK13 ADAT1 PEX11A MMS19 INTS10 RNASEL PEX7 CDK12 ADCK1 ZNF223 SUGP2 INTS12 RNF185 PES1 CCDC66 FAM13A ZNF232 MORC2 INTS3 RNF14 PET117 CDK11A TUBA1C ZNF235 MORF4L1 INTS4 RNASET2 PEX1 CDIPT FAM135A PER3 MOV10 INTS7 RNF103 PEX11B CAMTA2 ADCK3 ZNF599 SUFU IP6K1 SLC27A3 PEX19 CAMTA1 FAM134A ZNF600 MON2 IP6K2 RNF111 PEX5 CNTROB FAM133B PELI3 MOK IPO11 RNF13 PEX6 WASF2 ADCY3 PDZRN3 MNAT1 HSPBP1 RNF130 FBXO42 C3orf58 ZNF765 ANK2 MNDA HEATR5B RNF135 HIF1AN ZMIZ2 ZNF777 SLC30A4 MOB1B HDHD3 RNF138 BTBD7 ZMIZ1 ADAM15 ZNF273 MOCS2 HDLBP SLC18B1 CTC1 WASH4P TTLL4 AMOTL2 SULF2 HEATR5A RPL8 BTD ZMAT1 TTLL5 ZNF169 MOGS HEATR6 RPN1 ZNF302 ZKSCAN8 ZNF778 SLC38A1 MTMR12 HECA RPN2 VAV2 C4orf3 TTYH3 ANPEP MTMR14 HECTD1 RPL7A CTBP2 C4orf33 ADAM28 RNASE4 MTMR4 HECTD3 RPP38 BTN3A1 WBP11 FAM160B1 PHLDB1 MTMR6 HECTD4 RPRD1B VCAM1 CNST ADAM9 RCSD1 MTO1 HEG1 RPRD2 ZNF304 ZKSCAN5 FAM160A2 ALS2CL MTMR10 HDAC9 SIN3B ZNF317 CNTRL ADCY4 SNX10 MTOR HIPK1 SIN3A BROX ZMYM4 ACIN1 ALPL MTPAP HCFC1 RPL7L1 BRPF1 WARS2 FAM129B RNF144A MTRR HCFC2 SLC18A2 BRPF3 WAS ZNF721 ANGPTL2 MTMR11 HCK SIPA1 BRWD1 COIL FAM107B PDE4B MTMR1 HCLS1 RPL5 BRWD3 ZMYM3 ADH5 PDE4A MTF2 HDAC8 RPS10 ZNF319 COG4 FAM105A PDE1B MTFP1 HDAC4 RPS6KA1 BTAF1 COG3 ADHFE1 SLC35F2 MTFR1 HDAC6 RPS6KA2 ZNF318 ZMYM2 FAM102A RERG MTM1 HDAC7 RPS6KA3 CTAGE5 COASY TUBB6 REPS2 MTHFD2L HELZ RPS6KA4 ZNF28 ZMPSTE24 ADIPOR1 ANO8 MTHFR TMEM67 RPS6KB1 CSTF1 ZKSCAN1 FAHD2A ANKS6 MTIF2 TMEM69 RPS6KC1 VIM WDFY1 ADIPOR2 SLC35G1 MTSS1L HIBADH SIMC1 C11orf49 ZFYVE26 ZNF746 ZNF618 MVK HID1 RPTOR ZNF275 C6orf120 ADD3 REEP6 MVP HIGD1A RPS3 CSRP1 WDFY3 FAM129A SLC2A10 MX1 HELZ2 RPS27L CSRNP2 ZFYVE16 ADCY7 SLC41A2 MYADM HIGD2A RPS15 ZNF280D CMTR2 FAM126A C7 MTX1 HINFP RPS15A VCP CMTR1 ADD1 RPS6KL1 STRA13 HINT2 SLAIN1 BUD13 C6orf203 FAM120B NTN4 MYBBP1A HIP1 SLA BZW2 ZFYVE1 FAM120AOS CAMSAP2 MYCBP2 HEMK1 SIRT3 C10orf10 C6orf226 FAM118B BCAT1 STOML2 HERC1 SKI ZNF292 ZFX FAM118A ZNF521 MUTYH HERC2 RP2 ZNF286A CMTM3 FAM117A ZNF763 MTX3 HERC3 SIRT7 VGLL4 WDPCP FAM111A ZC4H2 STUB1 HERC5 SLC16A3 C10orf54 C5orf42 ZNF821 BCAR1 STT3A HERC6 SLC12A9 ZNF282 CNOT6L TTC3 PORCN STRN4 HERPUD2 SLC12A7 BRIX1 CNOT6 ZNF816 ADAMTSL4 STRN3 TMEM99 SLC12A6 CUTC CNOT4 ACSF2 ADAMTSL3 STRIP1 GUF1 SLC12A4 CUL9 CNOT3 ACSF3 ADAMTS9 STRBP GUSB SLC12A2 CUL7 ZHX3 FAM216A RSAD2 STRADB GXYLT1 SLC10A7 CUL5 ZHX2 ACSL1 ADAMTS2 MUS81 TMX2 SLC10A3 CUL4B CNOT10 FAM214B NRSN2 MUT TMX1 SIRT1 CUL4A CNOT1 FAM214A BCL6B MS4A6A GYS1 RPL22 CUL3 CNN2 ACSL3 PODXL STXBP5 GZF1 SIPA1L1 CUL1 ZMYND11 FAM210B NUDT13 STXBP4 TMX4 RPL10A CUEDC2 COPS7A FAM210A ZDHHC11 STXBP3 GTF3C1 RPA1 UTP6 COPS4 ACSL4 ZDHHC1 STXBP2 GTF3C3 RPA3 UTRN COPRS ACSL5 CALCRL STX8 GTF3C4 RPAP1 BPGM COPG2 FAM208B ARHGEF19 STX4 GTPBP1 RPAP2 UVRAG COPA FAM208A ARHGEF25 MSH2 GTPBP10 RPE BPHL COQ2 FAM206A ZNF74 MSH3 GTPBP2 RPF1 ZNF33B COMMD8 ZNF808 RAB11FIP5 MRPS9 GTPBP3 RPGR ZNF33A ZNF175 ZNF823 BCO2 MRPS23 TNFAIP3 SIPA1L2 CUX1 C1orf35 ACP6 ZNF77 MRPS27 TNFAIP2 RPH3AL ZNF335 COTL1 FAM222B NRP2 MRPS31 TNFAIP1 RPIA BMP2K C1orf50 ACKR3 ADAMTS10 MRPS5 H2AFY PPP1R3B ZNF350 CORO1C ACLY NPR2 MSH6 HAUS1 NRIP1 UTP14C CORO1A ACO1 NPNT MTDH HAUS3 NRP1 ZNF35 ZNF17 ACO2 ZC3H12A MT-ND6 HAUS4 NSDHL UTP18 ZNF160 ACOT1 ZNF786 MTA1 HAUS6 NSFL1C BMS1 COQ5 FAM227B ZBTB8A MTA2 HBB NSMAF CXCL12 C1QA ACOT13 NPHP4 MT-ND3 TMPO NRDE2 BNIP2 C1QB ACOT2 ARMCX2 MSL1 HARS2 NR1D2 BNIP3L COL18A1 ACOT7 SAMD4A MSL3 HARS NR1H3 BOD1L1 C21orf59 ACP5 SAMD9 MSRB1 H2AFZ SRRM2 ZNF343 ZNF124 ACOT8 ACTG2 MST1 H6PD SRRM1 UTP2O ZNF121 ACOT9 ZNF783 MSTO1 HACE1 NR2C1 CWF19L2 ZNF117 TTC27 SMOC2 MT-ATP6 HACL1 NR3C1 CWF19L1 C2CD3 ACOX1 SMO MT-ATP8 HADHB NR4A1 CWC27 ZNF106 FAM220A CARD10 MT-CO3 HIP1R NR4A2 CWC22 ZNF101 FAM21C RTP4 MT-CYB HIPK2 SRR ZNF337 VWA9 FAM21A ZNF780A MAST4 TMEM254 NRAS CTNNBL1 C2orf47 ACOX3 ZNF780B MARK2 HP1BP3 NRBP1 CTNNB1 ZNF10 ACP1 ACVRL1 MARK3 TMEM256- NSMCE4A BRD4 C2orf49 ACP2 ZNF41 PLSCR3 MARK4 HPRT1 NUDC VAC14 COL1A2 ACSS1 NR3C2 MARS HPS3 SRGN CTNNA1 COL1A1 FAM200B PPIC MAST3 HPS4 NUB1 CTIF C21orf33 ZNF785 CADPS2 MASTL HRAS NUBP2 BRE COMMD7 TTF1 PODN MAT2A HIPK3 NUBPL BRF1 COMMD3 TTF2 PLEKHH2 MATN2 HNRNPUL2 NUCB2 BRF2 COLGALT1 TTI1 C8orf58 MAVS HOOK3 NSRP1 CTDSPL ZNF142 FAM179B RAI14 MAPKAPK2 TMEM39B SRI CTDP1 C1R FAM175B ARAP2 MAPK7 TMEM248 NTPCR VAMP2 C1RL ACVR1B SPIN3 MAPK8IP3 HS1BP3 NSUN2 CTNND1 C1S FAM173B SNED1 MAPKAPK3 HSP90B1 NSUN4 ZNF333 VWA5A ACSS2 SPIRE1 MARCH7 TMEM222 SRP54 ZNF331 VWA8 ZNF789 BMPR2 MAPKBP1 TMEM219 SRP19 ZNF329 COL6A2 ACTA2 PLLP MARCH2 HSP90AB1 NR1D1 BRAF ZNF134 ACTB PLS3 MARCH6 HSPA13 SRRT CTSF ZNF133 ACTG1 SPRED1 MBD1 HSPA5 NONO BRAP CHN2 TTC37 ZFHX3 MCM2 HSDL2 NOP56 CTSC ZDHHC20 ACTL6A OLFML3 MCCC2 TMEM241 NOMO1 CTSB ZDHHC17 FAM199X RAI2 SYNCRIP HSD17B4 NOS3 CTSA ZDHHC16 ZNF791 NUP210 SYMPK HNRNPK NOTCH1 BRAT1 ZDHHC13 TTC39B C8orf44 SYK HIVEP2 NOTCH2 BRCA1 WDR77 TTC39C OSCP1 MCM6 HK1 NOMO2 UXS1 CKAP5 FAM193B AIM1 MCM8 HLTF SSRP1 BRD1 CACTIN FAM193A APOL4 MCM9 HLA-DRB1 NNT CTR9 CACUL1 FAM189B RAPGEF5 MCMBP HIVEP1 NOA1 CSRNP1 CAD FAM188A OSBPL7 MCAM HIRA NOB1 CSPP1 WDR81 TTC7A OSBPL3 SYNE1 HIST1H1C NOC2L ZNF217 CALCOCO2 TTC7B PLEKHA4 SYNJ1 TMEM63B NOC4L C19orf47 ZCWPW1 EIF5 PLEKHA7 MBD4 TMEM62 NOD1 CPVL CLASP1 CD2BP2 RAP1GAP2 MBD5 HLCS NOLC1 CPT1B CA5B ZNF500 SLAMF8 MBIP HMOX2 NOL10 CPT1A ZDHHC8 ZNF529 SLAMF7 SYNGR2 TMEM45A NOL6 CPSF7 WDR7 ARHGAP1 RANBP17 MBNL1 TMEM44 NOL8 CPSF1 WDR70 UGCG C8orf4 MBOAT2 HM13 NOL9 CRADD CLCN7 ARHGAP10 PLEKHG4 MBTPS1 HNRNPC SSH1 CPQ CLCN6 ARHGAP12 AQP3 MBTPS2 HNRNPD SSBP4 CREBRF CAB39L ZNF502 SPRY4 SYTL4 HNRNPDL NPM3 CREBBP CABIN1 ARHGAP17 PLVAP SYTL2 HMCES SRSF9 ZNF224 CLCN2 ARHGAP19 OLFM2 MAGED2 HMG20A SRSF5 CREB3L2 CABLES1 ARHGAP21 BIN2 MAN2A1 HMGB1 NPIPB3 C17orf75 WDR73 ARHGAP26 CACHD1 MALT1 STOML1 NPC1 ZNF222 WDR74 ARFIP1 RAB3D MAML1 RAN NPDC1 C18orf25 WDR75 ARFGEF1 BICC1 MAML3 RANBP10 NPHP3 CRAT CALD1 APOBEC3G ZNF708 MAN1A1 RANBP2 NPIPA2 ZNF211 CHRNB1 AREL1 NUTM2D MAN1B1 RANBP6 ORC3 CPPED1 CAMK1 ARFGAP3 CACNB1 SYVN1 RANBP9 SPICE1 VTA1 CAMK1D ZNF493 CACNB3 SZT2 RAP1A SPHK2 COX6A1P2 ZCCHC4 DTX3 ADORA2A TAF1 RALY ORMDL2 ZNF180 WHAMM ZNF496 PNPLA7 TADA3 RAP1GDS1 OSBPL10 C1orf216 ZCCHC2 DMXL1 BHLHB9 TADA1 RAPGEF1 SPNS1 ZNF207 CHPF2 DMXL2 ADIRF TACC1 RAPGEF2 SPPL3 ZNF197 ZCCHC14 ARHGAP9 BGN MAN2A2 RAPGEF3 SPRY1 VPS54 WHSC1 UBE2V2 ZNF704 MAP3K8 SLC43A2 SPRED2 CPNE8 WDR82 ARHGEF10 NYNRIN MAP3K13 RAD52 OPA1 C1GALT1 CHST11 DNAH1 PLXNA1 MAP3K2 RAD54L2 SPNS2 VPS72 CIC ARHGEF10L OGN MAP3K4 RAE1 SPOPL C1GALT1C1 CALM2 ARHGEF11 PLXNA2 MAP3K5 SLC43A3 SPOP ZNF202 ZCRB1 ARHGEF12 RAD51AP1 MAP3K7 RAF1 SPON2 ZNF200 WDR90 ZNF507 SIPA1L3 MAP4 RAI1 SPOCK2 CPNE2 ZCCHC8 EIF4H PMEPA1 MAN2B1 RALBP1 OTUD5 VPS8 CHST15 DROSHA ARHGAP25 MAP4K2 RALGAPA1 OTUD6B CPEB3 WDR91 UBE2V1 ZNF354C MAP4K4 RALGAPA2 SPDL1 CPEB2 ZDHHC9 UFSP2 ZNF701 MAP7 RALGAPB OSBPL5 CPD ZEB1 ASAP1 BLNK MAP7D1 RALGDS OXLD1 VRK3 C6orf89 ARHGAP30 CA2 MAP3K12 RAPGEF6 OXSM VSIG10 ZFP64 ZNF503 ARHGAP29 MAP3K1 RBBP8 OXSR1 VPS41 CLPTM1L DST OBSCN MAN2C1 RB1 SPATS2L CRELD1 CLPTM1 UFL1 SPTLC3 MANBA RB1CC1 SPECC1L CSK WDR18 ARHGAP32 ARHGAP31 MANSC1 RBBP5 OSBPL8 VOPP1 C8orf33 ARHGAP33 TLDC1 MAP1S RBBP6 OSBPL9 C12orf73 CLNS1A UBE2R2 L3MBTL1 MAP2K1 RBBP9 OSMR VPS13A CLN6 ARHGAP35 CX3CL1 MAP2K2 RARA SPG21 ZNF251 CLN3 ZNF528 UST MAP2K3 SLC39A9 SPG20 CSF3R CLK4 ARVCF TGM2 MAP2K4 RBL1 SPG11 VPS13B CLK2 ARHGAP4 CYB561D1 MAP2K6 RBL2 SPEN VPS13C CLK1 ZNF527 KLRK1 MCOLN1 RBM10 SPEF2 ZNF250 CLIP2 ARHGAP5 THBS2 MFSD6 RBM12 NUP62 CSF1R CLSTN1 ARCN1 THNSL1 MFSD9 RARS NUP88 CSF1 C7orf26 ARAP3 THNSL2 MFSD1 RASA2 NUP93 CSE1L C7orf43 UBE2Q2 KLHL26 MGA RASA4 NUP98 VPS13D CLYBL DYM KLHL23 MGAT4A SLC40A1 SRF CRYZ CLUH DVL3 KLHL17 MGAT4B RASGRP3 SRD5A1 ZNF253 CLUAP1 ASNS CYP2U1 MFNG RASL11A SREK1 CSNK2A1 CLU DUSP22 CYP4F12 METTL25 RAD51D SREBF2 CSNK1E CLTC DUSP6 KIRREL METTL2A RAD51B SREBF1 CSNK1D CLSTN3 APOL2 CYR61 METTL4 SLC4A1AP NUP35 ZNF264 ZFP91 APOL3 LAMA4 METTL6 RAB18 NUP214 C12orf4 ZFP90 UBE2J2 CTTNBP2NL METTL7A RAD50 NUDT5 C12orf43 CLIP4 ASPH LAMB3 SUV39H2 QSER1 NUFIP1 ZNF254 CLIP1 DYRK4 LIMS2 MFAP4 QSOX1 NUMA1 C14orf159 WDR61 DLST LIMCH1 MFF R3HDM1 NUMBL VPS16 ZFAND4 DYRK1B LILRB4 MFHAS1 R3HDM2 NUP153 C16orf58 CLEC16A UHMK1 LILRB2 MGME1 RAB11FIP1 NUP155 C16orf62 ZFAND3 DYNLT3 LIFR MGMT RAB11FIP2 NUP160 ZNF236 WDR47 ZNF548 LGI4 MIER2 RAB11FIP3 NUP188 C16orf72 C9orf78 DYNC1LI2 VCAN MIER3 RAB3GAP1 NUP205 VPS37A ZFAND1 DYNC1LI1 VAV3 SURF1 RAB3GAP2 SRD5A3 VPS37B ZER1 DMAP1 VAV1 MIIP RAC1 OCIAD2 C16orf87 WDR59 ASPSCR1 LEF1 MINA RAB3IP OCRL ZNF23 ZEB2 DUSP23 LDOC1 MINK1 RACGAP1 ODC1 CRNKL1 WDR6 ASCC2 TEAD2 SUPV3L1 RADI ODF2 ZNF25 WDR60 AQP1 LDB2 SUPT5H RAD17 SPTAN1 CRYBG3 WDR44 UGGT2 TEF SUPT3H RABGAP1L OGDH C14orf28 WDR43 ASH1L TEK MIA3 RABGAP1 OGFOD1 CRY2 CLIC4 ZNF480 CTH MIB2 RABEPK OBSL1 CRTC2 CLIC2 ASF1A LARP6 MICAL1 RABEP2 SRCAP CRTAP CLHC1 UGGT1 KIF21A MICAL2 SLC46A3 NXPE3 C15orf39 WDR26 ASCC3 DENND5B MICAL3 RAB40C SQLE CROT CLEC7A ASCC1 DDR2 MICALL1 SLC45A4 SPTY2D1 CROCC WDR27 ASB8 KAZN METTL23 RABEP1 OAS1 BMP1 WDR3 AQR KATNAL1 MED10 RBM12B OAS3 CXCR4 WDR33 ARAP1 KALRN MED13 RBM14 OAZ2 DDOST C9orf142 ASB7 JAM2 MED13L RFTN1 NMT1 ZNF436 WDR35 UGDH TMC4 MED14 RFWD2 NAT9 ATP6V1H ZFC3H1 APPL2 ITPRIPL2 MED15 RFWD3 NAV1 ATP7A WDR37 APPL1 ITPR3 MED17 RFX1 NAV2 ATP8A1 WDR4 DUSP2 ITIH5 MED27 RFX5 NBAS ATP9A ZFAT DMKN ITGB7 MED18 RFX7 NBEAL1 DDI2 DDX18 DUSP16 ITGA9 MED19 SLC35E1 NBEAL2 ATP9B ERN1 APOL6 TLR3 MED21 RGP1 STAU1 ATR AK9 APOO ITGA4 MED22 SLC35B3 STAT5B ATRN AKAP1 UBE2O ITGA1 MED23 SLC35B2 NCAM1 ATRX AKAP11 ZNF473 ISLR MED24 SLC35E2 STAT3 DDHD1 ESF1 ZNF48 DHFRL1 MECP2 REST NCAPD2 ATXN1 AKAP12 APP IQSEC2 MCTP1 SLC35F5 NCAPD3 ATP6V0D1 AKAP13 DUS4L INTU MCUR1 RETSAT STAT6 DDX3X ESCO1 DUS3L TM4SF18 MDH1 REV3L NAPEPLD DDX24 ESAM UBE3C KCNE3 MDM1 REXO1 NANP DDX21 ZNF680 DOCK5 KDELC1 MDN1 RFC1 NAP1L4 DDX19A AKAP2 DOCK4 KIAA1958 MDP1 RFC2 NAPA DDX11 ERV3-1 UBR4 DAPK2 ME2 RFC3 NAPB DDX10 ZNF678 DOCK2 TIGD6 ME3 RFNG NARF ATXN2 AKAP7 ARL8B KIAA1217 METAP2 RGPD8 NARS DDX41 ERP44 ZNF518B TIGD7 SVIL RHOBTB2 NARS2 B3GALNT2 TWISTNB DNTTIP2 KIAA0513 MESDC2 SLC30A6 NAT10 DCTPP1 AK1 UBR5 KDR METAP1 RHOB NCAPG2 ZNF420 AIP DNPH1 DCHS1 METTL10 RHOBTB1 NCAPH2 B3GAT3 AIFM1 DOCK7 TLR2 METTL14 RHOBTB3 NCBP1 URB2 ZNF688 DOCK8 TIMP3 METTL17 SLC35B1 NCSTN DCP1B ZNF687 DOPEY1 KCNQ1 MEN1 RHOG NDC1 DCN ETV6 DNAJB6 KCNMA1 MED7 RHOT1 NDOR1 DCLRE1C ZNF684 ARL4A KCNJ8 MEF2A RHOT2 STARD5 DCLRE1A ETS1 UBXN2B TLE2 MEF2D SLC2A9 NDUFA10 URI1 AIFM2 UBR3 TLN2 SWT1 RHBDF2 NCOR2 DCK ETFA DOK4 TCEA3 MEGF6 RGS12 NCOR1 ZNF426 ETF1 DOCK9 INTS2 MEGF8 RGS14 NCOA6 B2M TWF2 ZNF516 TBXAS1 MEGF9 RGS3 STAT2 ATXN2L ESYT2 DNMT3A SYBU JMJD1C RBMX2 NCDN DDB1 ESYT1 ARNTL CLIP3 GMEB1 SLC39A4 NCF1 ZNF432 AKAP9 ARMCX4 MECOM TPD52 RBM5 NCF2 ATXN7 TXNDC5 DNMT1 ME1 TPCN2 RBMX NCF4 ATXN7L1 ERCC8 DNAJC3 CMKLR1 GMDS RBMXL1 NCK2 ATXN7L3 ERCC6L2 UBXN2A CMPK2 GMEB2 RBPJ NCKAP5L AUP1 ERCC6 DNAJC21 MCF2L GMIP SLC39A3 NCOA1 AUTS2 ERCC5 DNMBP CNKSR3 GMNN SLC39A10 NCOA2 AVL9 ERCC4 ZNF514 CNN1 GLTSCR2 SLC38A9 NCOA3 AXIN1 ERCC2 DNAJC13 SYNM GLRX5 SLC39A6 NAIP UROD TXNL1 ARMC5 SYNPO GLS RBM43 STK24 ATP13A1 ERC1 DNHD1 MARCH3 GNA11 RBM42 MYO18A ATP13A3 ZNF671 ARPC3 SYNPO2 TP53I11 RBM19 STK3 DERA ERBB2 ARMC9 MARCH1 TP53BP2 RBM23 MYO1D DEPDC5 ERAP2 ARPC2 CNTLN GNL2 RBM27 MYO1F DENND6A ERAL1 ZNF512B MAPK13 TP53BP1 RBM28 STK11IP ATP2A2 TXNRD1 DOPEY2 MAPK10 GNPTAB RBM3 MYO5A ATP2A3 EPT1 UCHL5 MAP3K10 GNPTG RBM33 MYO5C ATP2B1 ERG ARHGEF6 CLEC3B GOLGA4 RBM38 MYO9A ZNF440 ERGIC1 UBLCP1 MEIS2 GNG7 RBM4 MYO9B ATP2C1 AKNA DPYD MMRN2 TP53I13 RECQL5 MYOF DENND4C ERMP1 ARHGEF40 MMP2 GNAI2 RDH5 MYOM2 ZNF44 ERMARD DPY19L1 CHN1 GNAI3 RDX MYO10 ATP13A2 ERMAP ARHGEF7 MMACHC GNAS RECK MYNN DENND4A ERLIN1 DPP9 CHPF GNB5 RECQL MYH10 ATP11C TXNDC11 ARHGEF9 CHRD GNG2 REEP4 STK4 ATM TXNDC12 ARID1A WFS1 TPM2 SLC36A4 STK39 ATMIN ERGIC2 ARSB MID2 GFPT1 SLC36A1 MYH9 ATN1 TXNDC16 UBN1 MERTK GET4 REL STK38L DGKE ERICH1 UBN2 CKAP2 TRAF3IP3 RELA MYLK UPF1 ERI3 UBQLN1 SUSD1 GFM1 SLC38A10 STK11 DGKA ERI2 UBXN7 SUSD2 GFM2 RC3H1 NACC1 DGCR8 AKR1C1 DPYSL2 WDR76 TRAF3IP1 RC3H2 NAB2 DGCR2 AKR1C3 UBE4A CKS2 GFOD2 RCBTB1 NABP1 ATP10D EVA1C ARSG WDR5B GGA1 RCCD1 NACA ATP11B EXTL3 UBFD1 CLEC14A GGA2 RCN1 NACC2 UPF2 F2R ARHGEF18 WASF1 GGCX RCN2 STK10 DENND4B TUBGCP6 UBL3 COL12A1 TRAF3 RCOR1 NADK DENND3 F13A1 ARHGEF2 COL14A1 TRAF7 RCOR3 NADSYN1 DEF8 F11R UBL4A TANC2 GDAP1 PRKX NAF1 DECR1 AFF4 UBL7 CPE TRAK2 SMARCAL1 NAGLU DDX60L EZH1 DNAJB1 CPED1 TRAFD1 SMARCAD1 STIP1 DDX60 AFMID DPP8 LRRC8C GEMIN5 SMARCA4 MYSM1 DDX6 AGA DOT1L

Provided herein are systems and methods for calculating a mutational burden and/or deconvolution of the identities and proportions of cell types in a sample. In some instances, the mutational burden and/or deconvolved cell types are calculated at or above a statistical threshold. The accuracy, specificity, sensitivity, positive predictive value, negative predictive value, or any combination thereof may be determined for an assay for mutational burden and/or deconvolution, for example, by running the assay against a set of independent samples. True positive is a positive test result that detects the condition when the condition is present. True negative is a negative test result that does not detect the condition when the condition is absent. False positive is a test result that detects the condition when the condition is absent. False negative is a test result that does not detect the condition when the condition is present. Accuracy is defined as the sum of true positive and true negative divided by the sum of true positive, true negative, false positive, and false negative. Specificity is defined as true negative divided by the sum of true negative and false positive. Sensitivity is defined as true positive divided by the sum of true positive and false negative. Positive predictive value is defined as true positive divided by true positive and false positive. Negative predictive value is defined as true negative divided by the sum of true negative and false negative.

In some instances, deconvolved cell identities and proportions (of the identities) in a sample are calculated at an accuracy of at least 50%, 60%, 70%, 80%, 90%, 95%, 99% or more. In some instances, deconvolution is calculated at an accuracy of at least 50%, 60%, 70%, 80%, 90%, 95%, 99% or more for at least 100, 200, 300, 400, or 500 or more independent samples. In some instances, deconvolved cell identities and proportions (of the identities) in a sample are calculated at a sensitivity of at least 50%, 60%, 70%, 80%, 90%, 95%, 99% or more. In some instances, deconvolution is calculated at a sensitivity of at least 50%, 60%, 70%, 80%, 90%, 95%, 99% or more for at least 100, 200, 300, 400, or 500 or more independent samples. In some instances, deconvolved cell identities and proportions (of the identities) in a sample are calculated at a specificity of at least 50%, 60%, 70%, 80%, 90%, 95%, 99% or more. In some instances, deconvolution is calculated at a specificity of at least 50%, 60%, 70%, 80%, 90%, 95%, 99% or more for at least 100, 200, 300, 400, or 500 or more independent samples. In some instances, deconvolution has a correlation with the Gold Standard of at least 0.5, 0.6, 0.7, 0.8, 0.9, 0.95, 0.99 or more. In some instances, deconvolution has a correlation with the Gold Standard of at least 0.5, 0.6, 0.7, 0.8, 0.9, 0.95, 0.99 or more for at least 100, 200, 300, 400, or 500 or more independent samples.

In some instances, the mutational burden in a sample is calculated at an accuracy of at least at least 50%, 60%, 70%, 80%, 90%, 95%, 99% or more. In some instances, the mutational burden is calculated at an accuracy of at least 50%, 60%, 70%, 80%, 90%, 95%, 99% or more for at least 100, 200, 300, 400, or 500 or more independent samples. In some instances, the mutational burden in a sample is calculated at a sensitivity of at least at least 50%, 60%, 70%, 80%, 90%, 95%, 99% or more. In some instances, the mutational burden is calculated at a sensitivity of at least 50%, 60%, 70%, 80%, 90%, 95%, 99% or more for at least 100, 200, 300, 400, or 500 or more independent samples. In some instances, the mutational burden in a sample is calculated at a specificity of at least at least 50%, 60%, 70%, 80%, 90%, 95%, 99% or more. In some instances, the mutational burden is calculated at a specificity of at least 50%, 60%, 70%, 80%, 90%, 95%, 99% or more for at least 100, 200, 300, 400, or 500 or more independent samples. In some instances, the mutational burden has a correlation with the Gold Standard of at least 0.5, 0.6, 0.7, 0.8, 0.9, 0.95, or 0.99 or more. In some instances, the mutational burden has a correlation with the Gold Standard of at least 0.5, 0.6, 0.7, 0.8, 0.9, 0.95, or 0.99 or more for at least 100, 200, 300, 400, or 500 or more independent samples.

Therapeutic Applications

Provided herein are methods and systems for determining an immune-oncology profile using sequencing data, wherein the profile may be used for therapeutic applications. In some instances, the profile comprises immune modulatory molecule expression, cell type and ratio, and mutational burden. In some instances, the profile is determined for diagnosis of a disease or disorder. In some instances, the profile is determined for treatment purposes. For example, the profile is used to determine efficacy of a treatment regimen. In some instances, the profile is used to recommend a therapeutic intervention.

In some instances, determination of the immune-oncology profile occurs prior to a treatment, during a treatment, or after a treatment. In some instances, determination of the immune-oncology profile occurs one or more time points prior to a treatment, during a treatment, or after a treatment. Time points for the monitoring and response-to-treatment methods provided herein, include any interval of time. In some instances, the time points are 1 day, 2 days, 3 days, 4 days, 5 days 6 days, 1 week, 2 weeks, 3, weeks, 4 weeks, 1 month, 2 months, 3 months, 4 months, 5 months, 6 months, 7 months, 8 months, 9 months, 10 months, 11 months, 1 year, 2 years or longer apart. In some instances, samples are obtained at any number of time points, including 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, or more time points.

In some instances, the immune-oncology profile is used to determine a specific treatment for a disease or disorder subject. In some instances, a sample is a first sample obtained from a subject at a first time point. In some instances, the method further comprises determining the immune-oncology profile by determining the immune modulatory molecule expression, cell type and ratio, and mutational burden from a second sample obtained from the subject having the related disease or disorder at a second time point; and comparing the immune-oncology profile from the first time point to the second time point. Sometimes, immune-oncology profiles are generated for a subject at multiple time points, wherein the profiles are compared to evaluate the progression of a disease or disorder and/or a response to treatment.

In some cases, the methods and systems described herein are used for diagnosing or treating a disease or disorder, wherein the disease or disorder is cancer. In some instances, the cancer is a solid cancer or a hematopoietic cancer. Sometimes, a cancer targeted herein is a recurrent and/or a refractory cancer. In some instances, the cancer is an acute cancer or a chronic cancer. In some instances, the cancer is an accelerated refractory cancer. In some instances, the cancer is in remission. In some instances, the cancer is a stage I, stage II, stage III, or stage IV cancer. In some instances, the cancer is a juvenile cancer or adult cancer. Examples of cancers include, but are not limited to, breast cancer such as a ductal carcinoma, medullary carcinomas, colloid carcinomas, tubular carcinomas, and inflammatory breast cancer; ovarian cancer, including epithelial ovarian tumors and adenocarcinoma in the ovary; uterine cancer; cervical cancer such as adenocarcinoma in the cervix epithelial, squamous cell carcinoma and adenocarcinomas; prostate cancer, including adenocarcinoma; pancreatic cancer, including epitheliod carcinoma in the pancreatic duct tissue and adenocarcinoma in the pancreatic duct; bladder cancer, including transitional cell carcinoma, urothelial carcinomas, tumors in the urothelial cells, squamous cell carcinomas, adenocarcinomas, and small cell cancers; leukemia, including acute myeloid leukemia (AML), acute lymphocytic leukemia, chronic lymphocytic leukemia, chronic myeloid leukemia, hairy cell leukemia, myelodysplasia, myeloproliferative disorders, acute myelogenous leukemia (AML), chronic myelogenous leukemia (CML), mastocytosis, chronic lymphocytic leukemia (CLL), multiple myeloma (MM), and myelodysplastic syndrome (MDS); bone cancer; lung cancer, including non-small cell lung cancer (NSCLC) such as squamous cell carcinomas, adenocarcinomas, and large cell undifferentiated carcinomas, and small cell lung cancer; skin cancer, including basal cell carcinoma, melanoma, and squamous cell carcinoma; eye retinoblastoma; cutaneous or intraocular melanoma; primary liver cancer; kidney cancer; autoimmune deficiency syndrome related lymphoma, including diffuse large B-cell lymphoma, B-cell immunoblastic lymphoma and small non-cleaved cell lymphoma; Kaposi's Sarcoma; viral-induced cancers including hepatitis B virus (HBV), hepatitis C virus (HCV), and hepatocellular carcinoma; human lymphotropic virus-type 1 (HTLV-1) and adult T-cell leukemia/lymphoma; and human papilloma virus (HPV) and cervical cancer; central nervous system (CNS) cancers, including primary brain tumors such as astrocytoma, anaplastic astrocytoma, or glioblastoma multiforme, oligodendrogliomas, ependymomas, meningiomas, lymphomas, schwannomas, and medulloblastomas; peripheral nervous system (PNS) cancers, including acoustic neuromas and malignant peripheral nerve sheath tumors (MPNST) such as neurofibromas and schwannomas, malignant fibrous cytomas, malignant fibrous histiocytomas, malignant meningiomas, malignant mesotheliomas, and malignant mixed Müllerian tumors; oral cavity and oropharyngeal cancer such as hypopharyngeal cancer, laryngeal cancer, nasopharyngeal cancer, and oropharyngeal cancer; stomach cancer, including lymphomas, gastric stromal tumors, and carcinoid tumors; testicular cancer such as germ cell tumors (GCTs), which include seminomas and nonseminomas, and gonadal stromal tumors, which include Leydig cell tumors and Sertoli cell tumors; thymus cancer, including thymomas, thymic carcinomas, Hodgkin disease, non-Hodgkin lymphomas carcinoids or carcinoid tumors; rectal cancer; and colon cancer.

In some cases, the methods and systems disclosed herein for determining immune modulatory molecule expression, cell type and ratio, and mutational burden are used for treating cancer. For example, at least one of immune modulatory molecule expression, cell type and ratio, and mutational burden is determined prior to cancer treatment. In some cases, at least one of immune modulatory molecule expression, cell type and ratio, and mutational burden is measured in a sample. In some instances, the sample is obtained from tumor tissues. In some cases, the sample is obtained from non-tumor tissues. In some cases, the sample is obtained from a subject who has cancer or has been diagnosed with cancer. In some cases, the sample is obtained from subjects who have not been diagnosed with cancer. In some cases, the sample is obtained from subjects who are in remission. Following determination of an immune-oncology profile based on at least one of immune modulatory molecule expression, cell type and ratio, and mutational burden, a cancer treatment may be applied. Examples of treatments for cancer include, but are not limited to, chemotherapy, radiation, surgery, or immunotherapy.

In some instances, determination of the immune-oncology profile occurs in conjunction with surgery. For example, determination of the immune-oncology profile occurs prior to tumor surgery and/or following tumor surgery. In some instances, the immune-oncology profile is indicative of the efficacy of the surgery. The immune-oncology profile may be determined any time following surgery. In some instances, the immune-oncology profile is determined 1 day, 2 days, 3 days, 4 days, 5 days 6 days, 1 week, 2 weeks, 3, weeks, 4 weeks, 1 month, 2 months, 3 months, 4 months, 5 months, 6 months, 7 months, 8 months, 9 months, 10 months, 11 months, 1 year, 2 years, or more than 2 years following surgery. In some instances, the immune-oncology profile is determined at any number of time points, including 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, or more time points.

In some instances, determination of the immune-oncology profile occurs in conjunction with chemotherapy. For example, determination of the immune-oncology profile occurs prior to chemotherapy and following chemotherapy. In some instances, determination of the immune-oncology profile indicates the efficacy of the chemotherapy. Examples of chemotherapy includes, but are not limited to, cyclophosphamide, paclitaxel, 5-fluorouracil, 5-aza-2′-deoxycitidine, mitomycin, doxorubicin, and mitoxantrone. The immune-oncology profile may be determined any time following chemotherapy. In some instances, the immune-oncology profile is determined 1 day, 2 days, 3 days, 4 days, 5 days 6 days, 1 week, 2 weeks, 3, weeks, 4 weeks, 1 month, 2 months, 3 months, 4 months, 5 months, 6 months, 7 months, 8 months, 9 months, 10 months, 11 months, 1 year, 2 years, or more than 2 years following chemotherapy. In some instances, the immune-oncology profile is determined at any number of time points, including 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, or more time points.

In some instances, determination of the immune-oncology profile occurs in conjunction with radiation treatment. For example, determination of the immune-oncology profile occurs prior to radiation treatment and/or following radiation treatment. In some instances, the immune-oncology profile indicates the efficacy of the radiation treatment. The immune-oncology profile may be determined any time following radiation treatment. In some instances, the immune-oncology profile is determined 1 day, 2 days, 3 days, 4 days, 5 days 6 days, 1 week, 2 weeks, 3, weeks, 4 weeks, 1 month, 2 months, 3 months, 4 months, 5 months, 6 months, 7 months, 8 months, 9 months, 10 months, 11 months, 1 year, 2 years, or more than 2 years following radiation treatment. In some instances, the immune-oncology profile is determined at any number of time points, including 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, or more time points.

Alternately or in combination with surgery, chemotherapy, or radiation, determination of the immune-oncology profile occurs in conjunction with immune therapy. In some instances, the immune therapy comprises administration of a modulatory agent for an immune checkpoint. Examples of immune checkpoint targets include, but are not limited to, 2B4 (CD244), A2aR, B7H3 (CD276), B7H4 (VTCN1), B7H6, B7RP1, BTLA (CD272), butyrophilins, CD103, CD122, CD137 (4-1BB), CD137L, CD160, CD2, CD200R, CD226, CD26, CD27, CD28, CD30, CD39, CD40, CD48, CD70, CD73, CD80 (B7.1), CD86 (B7.2), CEACAM1, CGEN-15049, CTLA-4, DR3, GAL9, GITR, GITRL, HVEM, ICOS, ICOSL (B7H2), IDO1, IDO2, ILT-2 (LILRB1), ILT-4 (LILRB2), KIR, KLRG1, LAG3, LAIR1 (CD305), LIGHT (TNFSF14), MARCO, NKG2A, NKG2D, OX-40, OX-40L, PD-1, PDL-1 (B7-H1, CD 274), PDL-2 (B7-DC, CD 273), PS, SIRPalpha (CD47), SLAM, TGFR, TIGIT, TIM1, TIM3 (HAVCR2), TIM4, or VISTA. An immune checkpoint modulatory agent in some cases is at least one of a small molecule, an antibody, a nucleic acid encoding an antibody, an antigen binding fragment, a RNA interfering agent, a peptide, a peptidomimetic, a synthetic ligand, and an aptamer. In some instances, an immune checkpoint inhibitor is administered. Examples of immune checkpoint inhibitors are Enoblituzumab (e.g., MGA271), Ipilimumab (e.g., BMS-734016, MDX-010), Tremelimumab (e.g., CP-675, CP-675,206), Lirilumab (e.g., BMS-986015, IPH2102), BMS986016, Pembrolizumab (e.g., MK-3475, SCH 900475), Nivolumab (e.g., BMS-936558, MDX-1106, ONO-4538), Pidilizumab (e.g., CT-011, MDV9300), Atezolizumab (e.g., MPDL3280A, RG7446, RO5541267), BMS-936559 (e.g., MDX-1105), Durvalumab, Avelumab, and Bavituximab. In some instances, the immune therapy is CAR T cell or T cell receptor therapy.

Methods and systems provided herein for determination of an immune-oncology profile may be used for prediction of a clinical outcome in response to a therapy. In some instances, the therapy is surgery, radiation, chemotherapy, or immune therapy. In some instances, the immune-oncology profile is used to predict a level of resistance to one or more chemotherapeutic agents. In some instances, the prediction of a clinical outcome based on the immune-oncology profile has an accuracy, specificity, sensitivity, positive predictive value (PPV), a negative predictive value (NPV), or a combination thereof for a type of response. In some instances, the type of response is a positive response. In some instances, a positive response is partial remission (e.g., cancer/tumor has gotten smaller) or complete remission (e.g., all signs of cancer are gone) of the tumor. In some instances, a positive response is the cancer has stopped growing or expanding. In some instances, a positive response is a statistically higher survival rate for a treated subject population compared to an untreated subject population. In some instances, the survival rate is a 1 year, 2 year, 3 year, 4 year, 5 year, 6 year, 7 year, 8 year, 9 year, or 10 year survival rate. In some instances, the type of response is a negative response. In some instances, a negative response is the absence of a positive response. In some instances, a negative response is continued cancer progression or growth. In some instances, a negative response is the continued presence of the cancer. In some instances, a positive response is continued cancer progression or growth at the predicted rate for an untreated subject population. In some instances, a prediction of a clinical outcome (e.g., a positive or negative response) has a positive predictive value for a set of independent samples. In some instances, the PPV for a response to a therapy is at least or about 90% for at least 100 independent samples. A positive predictive value may be accurately determined in at least about 50%, 60%, 70%, 80%, 90%, 95%, or 99% of at least 100, 200, 300, 400, 500, 600, 700, 800, 900, 1000, 2000, 3000, 4000, 5000, 6000, 7000, 8000, 9000, or 10000 independent samples.

In some instances, a prediction is generated using a classifier. In some instances, the proportions of cell types/subtypes determined by deconvolution, mutational burden, immune modulatory molecule expression, or any combination thereof are associated with an outcome such as, for example, a clinical outcome, a diagnosis of disease, and/or a response to therapy. In some instances, the classifier is trained using data comprising one or more of cell type/subtype proportions, mutational burden, and immune modulatory molecule expression along with associated outcomes. In some instances, the classifier comprises a panel of cell type/subtype proportions that are predictive of an outcome. In some instances, the classifier comprises a panel of immune modulatory molecules predictive of an outcome. In some instances, the classifier comprises a panel of mutational burden predictive of an outcome.

Disclosed herein, in some instances, are systems and methods for generating and/or using a classifier to make a prediction of an outcome. The classifier can be a machine learning algorithm or model trained using data from the immune-oncology profile. The data utilized from the immune-oncology profile can include the cell type/subtype proportions or percentages (e.g., immune cell types and percentages in a tumor sample). Examples of the cell types or subtypes include M1 macrophages, M2 macrophages, CD19+ B cells, CD14+ monocytes, CD56+ NK cells, CD8+ T cells, Treg cells, CD4+ T cells, or any combination thereof. Additional examples of cell types or subtypes are found throughout the present disclosure. In some cases, the data includes expression of immune-inhibitory genes or immune escape genes which can include, for example, CTLA4, OX40, PD-1, IDO1, CD47, PD-L1, TIM-3, BTLA, ICOS, ARG1, or any combination thereof. The data can also, in certain cases, include mutational burden information relating to the sample.

The classifier or trained algorithm of the present disclosure may be used make a prediction. The prediction can be based on information from an immune-oncology profile of a sample such as at least one of percentage(s) of cell type(s)/subtype(s), level(s) of immune inhibitory or escape gene(s), or mutational burden. The prediction can comprise stratifying a sample into two or more categories. The prediction can relate to diagnosis and/or prognosis. The prediction can also be based on monitoring the success of treatment of disease. Predictions can also be based on quality of life or symptomatic response. As an example, the prediction for a tumor sample obtained from a subject includes a positive identification of the sample as pancreatic ductal adenocarcinoma (PDA). The prediction optionally also includes a corresponding prediction classifying the sample as having poor survival based on immune-oncology profile data including high PD-L1 expression level and high Treg cell percentage infiltrating the tumor sample. The categories or groups can correspond to various predicted outcomes such as predicted treatment outcome or responsiveness to treatment.

The classifier used to generate predictions includes one or more selected feature spaces such as cell type/subtype proportion/percentage, immune inhibitory gene expression level, and mutational burden. The values for these features obtained from a sample can be fed into the classifier or trained algorithm to generate one or more predictions. In some cases, the methods disclosed herein select for the variables that are of predictive value, for example, by culling the features to generate a feature subset used for generating predictions in the final classifier or model. Methods that reduce the number of variables or features can be selected from a non-limiting group of algorithms including principal component analysis (PCA), partial least squares (PLS) regression, and independent component analysis (ICA). In some cases, the methods disclosed herein analyze numerous variables directly and are selected from a non-limiting group of algorithms including methods based on machine learning processes. Machine learning processes can include random forest algorithms, bagging techniques, boosting methods, or any combination thereof. Methods may be statistical methods. Statistical methods can include penalized logistic regression, prediction analysis of microarrays, methods based on shrunken centroids, support vector machine analysis, or regularized linear discriminant analysis.

The classifier or trained algorithm of the present disclosure as described herein can comprise one feature space. The classifier or trained algorithm of the present disclosure as described herein can comprise two or more feature spaces. The two or more feature spaces may be distinct from one another. Each feature space can comprise types of information about a sample, such as cell type/subtype percentage, expression of immune inhibitory molecules or genes, or mutational burden. The accuracy of the classification may be improved by combining two or more feature spaces in a classifier rather than using a single feature space. In some cases, combining both cell type/subtype percentage and immune inhibitory gene expression results in superior accuracy than using those features individually. Sometimes, accuracy is further improved by incorporating mutational burden. Individual feature spaces may have different dynamic ranges. The difference in the dynamic ranges between feature spaces may be at least 1, 2, 3, 4, or 5 orders of magnitude. As a non-limiting example, the cell subtype percentage feature space may have a dynamic range between 0 and 100, and the immune inhibitory gene expression feature space may have a dynamic range between 0 and about 20.

A feature space can comprise a panel of cell types/subtypes and their percentage or proportion within a sample. A feature space can comprise a panel of immune inhibitory genes and their expression level. A feature space can comprise one or more representations of mutational burden. A panel of an individual feature space may be associated with an outcome such as, for example, responsiveness to treatment. For example, a positive response to an immunotherapy may be associated with certain immune cell types exceeding a threshold percentage within a tumor sample. As another example, a negative response to an immunotherapy may be associated with an immune-inhibitory gene such as PD-L1 exceeding a threshold expression level within a tumor sample. In some cases, the classifier or trained algorithm comprises a panel of cell type/subtype percentages comprising at least 1, at least 2, at least 3, at least 4, at least 5, at least 6, at least 7, at least 8, at least 9, at least 10, at least 11, at least 12, at least 13, at least 14, at least 15, at least 16, at least 17, at least 18, at least 19, at least 20, or at least 20 cell types/subtypes. The classifier can comprise a panel of immune-inhibitory genes comprising at least 1, at least 2, at least 3, at least 4, at least 5, at least 6, at least 7, at least 8, at least 9, at least 10, at least 11, at least 12, at least 13, at least 14, at least 15, at least 16, at least 17, at least 18, at least 19, at least 20, at least 21, at least 22, at least 23, or at least 24 genes.

The classifier of the present disclosure may be trained with a set of samples obtained from subjects. A set of samples can comprise samples from at least 5, 10, 15, 20, 25, 30, 35, 40, 45, 50, 60, 70, 80, 90, 100, 150, 200, 250, 300, 350, 400, 450, 500, 600, 700, 800, 900, 1000, 2000, 3000, 4000, 5000, or more subjects. In some cases, the classifier is trained on a limited sample set with no more than 5, 10, 15, 20, 25, 30, 35, 40, 45, 50, 55, 60, 65, 70, 75, 80, 85, 90, 95, or 100 samples. The classifier may be trained on a limited sample set with no more than 15-20 samples or no more than 20-30 samples. The accuracy of the classifier takes on even greater importance when the sample size is small. A significant factor in the accuracy of the classifier is the quality of the data parameters input into the classifier to generate the prediction or classification. Likewise, the quality of the data input used to train the classifier is important to its predictive ability. For example, a classifier trained on a training data set having cell subtype percentages that were inaccurately determined will incorporate this inaccuracy during the training, which compromises its predictive ability with regards to new samples. When the sample size is large, a few poor data points will not have a significant impact on the resulting classifier. However, in the case when sample size is small such as around 15-25 samples, a few poor data points can negatively impact the classifier's predictive ability to a significant degree. Accordingly, the methods disclosed herein utilizing RNA normalization techniques that account for quantitative differences in RNA content amongst different cell types help generate highly accurate cell type/subtype percentages, which in turn allow for the generation of classifiers that effectively generate predictions despite being trained on small data sets such as, for example, no more than 15, 20, 25, 30, 35, 40, 45, 50, or 60 samples. This capability is critical for small-scale studies such as, for example, Phase I/II clinical trials which often entail small sample sizes. Indeed, larger Phase II trials may have 60 subjects, but the experimental group may still be only 15-20 when accounting for controls (e.g., 20 negative placebo controls, 20 receiving traditional treatment, and 20 receiving experimental treatment).

Moreover, in certain instances, the methods disclosed herein utilize end-to-end sample processing and analysis for quality control. As an example, FFPE curls obtained from tumor tissues are obtained, processed, and sequenced via next generation sequencing in a continuous workflow. In this example, the features utilized by the classifier are all mined from the sequencing data. For instance, RNA expression data (RNASeq) is fed into a deconvolution algorithm to determine cell type/subtype percentages. Likewise, the expression levels of immune inhibitory genes are also obtained from the sequencing data. Mutational burden can also be determined from the sequencing data.

A classifier may generate a different prediction each time it is given new sample data. Using different samples on the same classifier can generate a different or unique output each time the classifier is run. Using the same samples on the same classifier can generate a different or unique output each time the classifier is run. The classifier may analyze a sample by comparing it against the panel of features predictive of an outcome or response. In some cases, the classifier carries out the comparing, statistical analysis, downstream analyses, or any combination thereof.

In some cases, the features (e.g., cell type percentages, immune escape gene expression, and mutational burden) are analyzed using feature selection techniques. Feature selection techniques can include filters for evaluating feature relevance by examining the data properties, wrappers that embed the model hypothesis within a feature subset search, or embedded protocols that build the search for an optimal feature set is built into a classifier algorithm. In some cases, the methods described herein comprise a feature selection step in which relevant features are selected for inclusion in the final classifier and/or irrelevant or low relevance features are culled or removed from the final classifier.

Examples of filters that can be beneficial for use in the methods of the present disclosure include parametric methods such as two sample t-tests, analysis of variance (ANOVA) analyses, Gamma distribution models, or Bayesian models. Filters can include model free methods such as Wilcoxon rank sum tests, rank products methods, random permutation methods, between-within class sum of squares tests, or threshold number of misclassification. In some cases, filters include multivariate methods such as bivariate analysis, correlation based feature selection methods, minimum redundancy maximum relevance, Markov blanket filter, and uncorrelated shrunken centroid methods.

Wrappers that may be beneficial for use in the methods of the present disclosure can include sequential search methods, estimation of distribution algorithms, or genetic algorithms. Embedded protocols that may be beneficial for use in the methods of the present disclosure can include random forest algorithms, weights of logistic regression algorithms, or weight vector of support vector machine algorithms.

The statistical results obtained from the methods described herein can provide the likelihood the prediction is accurate. In some cases, the prediction is presented as a diagnosis along with a likelihood of accuracy such as, for example, a prediction of a positive response to a therapeutic cancer treatment with at least a 70%, 75%, 80%, 85%, 90%, or 95% estimated accuracy. The predictions may be analyzed using statistical tools including students T test, two sided T test, Pearson rank sum analysis, hidden Markov model analysis, analysis of q-q plots, principal component analysis, one way analysis of variance (ANOVA), two way ANOVA, and other statistical methods.

Computer Systems

The present disclosure provides computer systems that are programmed to implement methods of the disclosure. FIG. 8 shows a computer system 801 that is programmed or otherwise configured to carry out executable instructions. The computer system may be programmed to process nucleic acid sequencing information to generate a classifier comprising a panel of genetic variations predictive of adverse response to chemotherapy, by associating the nucleic acid sequencing information with adverse response to chemotherapy. The computer system may be programmed with a classifier for analyzing genetic information to generate a prediction of an adverse response to one or more chemotherapeutic agents. The computer system 801 can regulate various aspects of the methods of the present disclosure, such as, for example, training the algorithm with the nucleic acid sequencing information of a set of samples to generate a trained algorithm or classifier. The computer system 801 may determine the positive predictive value of a classifier by analyzing a set of independent samples with the classifier and comparing the actual incidents of adverse response to the predicted risk of adverse response. The computer system 801 can be an electronic device of a user or a computer system that is remotely located with respect to the electronic device. The electronic device can be a mobile electronic device.

The computer system 801 includes a central processing unit (CPU, also “processor” and “computer processor” herein) 805, which can be a single core or multi core processor, or a plurality of processors for parallel processing. The computer system 801 also includes memory or memory location 810 (e.g., random-access memory, read-only memory, flash memory), electronic storage unit 815 (e.g., hard disk), communication interface 820 (e.g., network adapter) for communicating with one or more other systems, and peripheral devices 825, such as cache, other memory, data storage and/or electronic display adapters. The memory 810, storage unit 815, interface 820 and peripheral devices 825 are in communication with the CPU 805 through a communication bus (solid lines), such as a motherboard. The storage unit 815 can be a data storage unit (or data repository) for storing data. The computer system 801 can be operatively coupled to a computer network (“network”) 830 with the aid of the communication interface 820. The network 830 can be the Internet, an internet and/or extranet, or an intranet and/or extranet that is in communication with the Internet. The network 830 in some cases is a telecommunication and/or data network. The network 830 can include one or more computer servers, which can enable distributed computing, such as cloud computing. The network 830, in some cases with the aid of the computer system 801, can implement a peer-to-peer network, which may enable devices coupled to the computer system 801 to behave as a client or a server.

The CPU 805 can execute a sequence of machine-readable instructions, which can be embodied in a program or software. The instructions may be stored in a memory location, such as the memory 810. The instructions can be directed to the CPU 805, which can subsequently program or otherwise configure the CPU 805 to implement methods of the present disclosure. Examples of operations performed by the CPU 805 can include fetch, decode, execute, and writeback.

The CPU 805 can be part of a circuit, such as an integrated circuit. One or more other components of the system 801 can be included in the circuit. In some cases, the circuit is an application specific integrated circuit (ASIC).

The storage unit 815 can store files, such as drivers, libraries and saved programs. The storage unit 815 can store user data, e.g., user preferences and user programs. The computer system 801 in some cases can include one or more additional data storage units that are external to the computer system 801, such as located on a remote server that is in communication with the computer system 801 through an intranet or the Internet.

The computer system 801 can communicate with one or more remote computer systems through the network 830. For instance, the computer system 801 can communicate with a remote computer system of a user (e.g., a laptop or a smart phone). Examples of remote computer systems include personal computers (e.g., portable PC), slate or tablet PC's (e.g., Apple® iPad, Samsung® Galaxy Tab), telephones, Smart phones (e.g., Apple® iPhone, Android-enabled device, Blackberry®), or personal digital assistants. The user can access the computer system 801 via the network 830.

Methods as described herein can be implemented by way of machine (e.g., computer processor) executable code stored on an electronic storage location of the computer system 801, such as, for example, on the memory 810 or electronic storage unit 815. The machine executable or machine readable code can be provided in the form of software. During use, the code can be executed by the processor 805. In some cases, the code can be retrieved from the storage unit 815 and stored on the memory 810 for ready access by the processor 805. In some situations, the electronic storage unit 815 can be precluded, and machine-executable instructions are stored on memory 810.

The code can be pre-compiled and configured for use with a machine having a processer adapted to execute the code, or can be compiled during runtime. The code can be supplied in a programming language that can be selected to enable the code to execute in a pre-compiled or as-compiled fashion.

Aspects of the systems and methods provided herein, such as the computer system 801, can be embodied in programming. Various aspects of the technology may be thought of as “products” or “articles of manufacture” typically in the form of machine (or processor) executable code and/or associated data that is carried on or embodied in a type of machine readable medium. Machine-executable code can be stored on an electronic storage unit, such as memory (e.g., read-only memory, random-access memory, flash memory) or a hard disk. “Storage” type media can include any or all of the tangible memory of the computers, processors or the like, or associated modules thereof, such as various semiconductor memories, tape drives, disk drives and the like, which may provide non-transitory storage at any time for the software programming. All or portions of the software may at times be communicated through the Internet or various other telecommunication networks. Such communications, for example, may enable loading of the software from one computer or processor into another, for example, from a management server or host computer into the computer platform of an application server. Thus, another type of media that may bear the software elements includes optical, electrical and electromagnetic waves, such as used across physical interfaces between local devices, through wired and optical landline networks and over various air-links. The physical elements that carry such waves, such as wired or wireless links, optical links or the like, also may be considered as media bearing the software. As used herein, unless restricted to non-transitory, tangible “storage” media, terms such as computer or machine “readable medium” refer to any medium that participates in providing instructions to a processor for execution.

Hence, a machine readable medium, such as computer-executable code, may take many forms, including but not limited to, a tangible storage medium, a carrier wave medium or physical transmission medium. Non-volatile storage media include, for example, optical or magnetic disks, such as any of the storage devices in any computer(s) or the like, such as may be used to implement the databases or other components shown in the drawings. Volatile storage media include dynamic memory, such as main memory of such a computer platform. Tangible transmission media include coaxial cables; copper wire and fiber optics, including the wires that comprise a bus within a computer system. Carrier-wave transmission media may take the form of electric or electromagnetic signals, or acoustic or light waves such as those generated during radio frequency (RF) and infrared (IR) data communications. Common forms of computer-readable media therefore include for example: a floppy disk, a flexible disk, hard disk, magnetic tape, any other magnetic medium, a CD-ROM, DVD or DVD-ROM, any other optical medium, punch cards paper tape, any other physical storage medium with patterns of holes, a RAM, a ROM, a PROM and EPROM, a FLASH-EPROM, any other memory chip or cartridge, a carrier wave transporting data or instructions, cables or links transporting such a carrier wave, or any other medium from which a computer may read programming code and/or data. Many of these forms of computer readable media may be involved in carrying one or more sequences of one or more instructions to a processor for execution.

The computer system 801 can include or be in communication with an electronic display 835 that comprises a user interface (UI) 840 for providing, for example, reports or results of risk stratification analysis of the nucleic acid sequencing information of a sample. Examples of UI's include, without limitation, a graphical user interface (GUI) and web-based user interface.

Methods and systems of the present disclosure can be implemented by way of one or more algorithms. An algorithm can be implemented by way of software upon execution by the central processing unit 805. The algorithm can, for example, analyze the nucleic acid sequencing information obtained from a sample to stratify a risk of adverse response to chemotherapy (e.g., one or more chemotherapeutic agents) for the subject from whom the sample was obtained.

While preferred embodiments of the present invention have been shown and described herein, it will be obvious to those skilled in the art that such embodiments are provided by way of example only. It is not intended that the invention be limited by the specific examples provided within the specification. While the invention has been described with reference to the aforementioned specification, the descriptions and illustrations of the embodiments herein are not meant to be construed in a limiting sense. Numerous variations, changes, and substitutions will now occur to those skilled in the art without departing from the invention. Furthermore, it shall be understood that all aspects of the invention are not limited to the specific depictions, configurations or relative proportions set forth herein which depend upon a variety of conditions and variables. It should be understood that various alternatives to the embodiments of the invention described herein may be employed in practicing the invention. It is therefore contemplated that the invention shall also cover any such alternatives, modifications, variations or equivalents. It is intended that the following claims define the scope of the invention and that methods and structures within the scope of these claims and their equivalents be covered thereby.

EXAMPLES

The following examples are given for the purpose of illustrating various embodiments of the disclosure and are not meant to limit the present disclosure in any fashion. The present examples, along with the methods described herein are presently representative of certain embodiments, and are not intended as limitations on the scope of the disclosure. Changes therein and other uses which are encompassed within the spirit of the disclosure as defined by the scope of the claims will occur to those skilled in the art.

Example 1: Classification of a Tumor Microenvironment

A tumor microenvironment was characterized by determining immune modulatory molecule expression levels, cell type and ratio, and tumor mutational burden.

RNA Extraction

RNA was extracted from formalin fixed paraffin embedded (FFPE) samples using the RNeasy kit (Qiagen) according to manufacturer's instructions.

Generation of Sequencing Library

Following RNA extraction, a sequencing library for next generation sequencing was generated according to manufacturer's instructions (Illumina). Coding regions were captured using Illumina Access kits.

Next Generation Sequencing

The enriched genes were sequenced on an Illumina's NextSeq sequencing machine to generate sequencing data and expression data.

Inhibitory Molecule Expression

The sequencing and expression data is used to determine the expression level of selected immune modulatory molecules including PD-1, PD-L1, CTLA-4, OX40, TIM-3, BTLA, ICOS, CD47, IDO1, and ARG1.

Cell Type and Ratio Deconvolution

Following next generation sequencing, sequencing data was analyzed for cell type and by ratio deconvolution. The use of next generation sequencing to generate sequencing and expression data for use in deconvolving cell types/subtypes as described herein is a new approach that provides superior performance compared to, for example, conventional gene expression systems such as those using microarrays. In addition, routine studies looking at immune cell percentages in tissue use a conventional approach of utilizing public databases of microarray expression data, which may be able to identify changes in cell proportions between different samples, but are ineffective for accurately determining the true percentage of a cell type/subtype in a given sample.

Ratio deconvolution was carried out using a deconvolution matrix comprising a set of cell expression signatures or “fingerprints.” The cell expression signatures or “fingerprints” were generated using sequencing data obtained from samples substantially composed of specific cell types (e.g., a CD4+ naïve cell fingerprint obtained from a purified population of CD4+ naïve cells). The cell-specific fingerprints were then placed into the deconvolution matrix. This matrix was then applied to the complex data set of RNA sequencing and gene expression data to allow for identification of cell types in the data and the relative proportions of each cell type. Included in the cell expression signatures or fingerprints were genes that were significantly differentially expressed in pairwise cell type differential expression analysis as well as those genes that were expressed at a consistent level within cell type across biological replicates.

Ratio deconvolution was also performed. The process of determining individual components from bulk sequencing and expression profiles was accomplished by solving the matrix equation: Ax=b where A was the cell expression fingerprints, x was the cell percentages, and b was the bulk expression counts. A vector regression method with data normalization was performed. See FIG. 3. Briefly, to deconvolve a mixture with N cell types using M genes, the problem is set up according to FIG. 3. Cell fractions were determined and normalization across rows was performed. The expression counts of each gene were normalized to be in the range of 0 to 1 across each cell type and the sample in question such as a mixture of cells. All genes were weighted equally regardless of their absolute expression value.

Tumor Mutational Burden Calculation

Tumor mutational burden was calculated. Following RNA sequencing, all the variants including somatic and germline were determined as shown in FIG. 4A with the variants indicated by the dark squares along the representative gene sequences. Total somatic mutational burden was thus determined without use of a paired normal. A panel of genes (˜4000) was then used for subsequent analysis since they were determined to correlate with mutational burden across the genome. This concept is illustrated in FIG. 4B in which the correlated genes A, C, and F are circled. Several germline variation databases were used to identify the initial variant calls that were germline variants based on a frequency of greater than 0.01%, and the identified germline variants were then excluded from mutational burden analysis. As shown in FIG. 4C, the excluded germline variants are crossed out with an “X”. From the remaining variants (which are circled in FIG. 4D) on the panel of genes, the total somatic mutational burden was extrapolated.

Tumor Microenvironment Summary Report

Data from the immune modulatory molecule expression, cell type and ratio deconvolution, and tumor mutational burden calculation was then compiled to generate a summary of these metrics in the tumor microenvironment. The summary was presented in an immune-oncology profile that displayed the information in a graphical output. The immune modulatory molecule expression was displayed in a bar graph alongside a reference or control expression level. A general breakdown of the cell types (immune, tumor, and stromal cells) and their relative percentages/proportions of the overall cell population in the sequenced sample were displayed in a pie chart. A more specific breakdown based on the percentages of specific cell types (T cells, CD4+ cells, myeloid cells, NK cells, and B cells) and cell sub-types (e.g., CD4+ and CD8+ T cells) in the sample was graphically displayed. Finally, the mutational burden was displayed as an indicator or marker on an axis ranging from low mutational burden (0 mutations per Megabase) to high mutational burden (2000 mutations per Megabase).

Example 2: Mutational Burden Analysis

Genes that provide improved resolution and accuracy for mutational burden analysis were determined. All the human genes were ranked in order using a weighted average of their likelihood to be mutated using data from public databases as well as by their consistency of expression across multiple tissues. Three different cancer types were analyzed with about 50 samples of each cancer. The accuracy was determined with an increasing number of genes from Table 5.

From Table 6, correlation with a Gold Standard mutational burden increased with about 2000 genes and then started to plateau. Mutational burden was compared to the Gold Standard mutational burden calculated using paired normal analysis of DNA. Specifically, the Gold Standard mutational burden measures somatic mutations using DNA sequence data obtained from the sample by comparing allele frequencies in normal and tumor sample alignments, annotating the identified mutations, and aggregating the mutations.

TABLE 6 Correlation with Gold Standard Genes HNSC Lung Breast 100 0.65 0.32 0.46 250 0.75 0.54 0.82 500 0.84 0.58 0.84 1000 0.87 0.7 0.9 2000 0.9 0.85 0.91 4000 0.93 0.91 0.91

Example 3: Characterization of a Glioblastoma Tumor Microenvironment

Using similar methods as described in Examples 1-2, a glioblastoma tumor microenvironment was characterized. As seen in FIG. 5A, different cell types were on the y-axis, while genes were on the x-axis. Gene expression level was represented by color with a darker purple color indicating relatively higher expression. In black and white, the darker shade indicates higher expression, while the lighter shade indicates lower expression. Gene 406 was identified as distinguishing a glioblastoma cancer cell type and immune cell types.

A similar gene matrix was also generated using about 800 genes (FIG. 5B). Referring to FIG. 5B, expression levels of multiple genes was determined and used to characterize the glioblastoma tumor microenvironment. The genes listed on the y-axis in FIG. 5B from top down include gbm, gMDSC, DCs, mMDSC, B-cell, Th2, Th17, Th1, Naïve-CD4-pos, Naïve-CD8-pos, CM-CD4-pos, Tregs, CM-CD8-pos, EM-CD8-pos, Stromal, M1, M2a, M2b, and M2c. The legend in FIG. 5B shows decreased expression indicated by a blue color, increased expression indicated by a red/orange color, and white being neutral or no change in expression. Most of the visible expression data indicates no change or increased expression.

Example 4: Characterization of Tumor Microenvironment for Various Types of Cancers

A tumor microenvironment was determined for various cancer types. Using similar methods as described in Examples 1-2, expression levels of multiple genes was identified in colorectal and blood cancers (FIG. 6). Gene expression levels were used to characterize the colorectal and blood cancer microenvironment. The genes listed on the y-axis in FIG. 6 for colorectal cancer from top down include B-cell, CD4-pos, CD8-pos, gMDSC, Macrophage, DCs, mMDSC, and stromal. The genes listed on the y-axis in FIG. 6 for blood from top down include gbm, gMDSC, DCs, mMDSC, B-cell, Th2, Th17, Th1, Naïve-CD4-pos, Naïve-CD8-pos, CM-CD4-pos, Tregs, CM-CD8-pos, EM-CD8-pos, Stromal, M1, M2a, M2b, and M2c. The legend in FIG. 6 shows decreased expression indicated by a blue color, increased expression indicated by a red/orange color, and white being neutral or no change in expression. Most of the visible expression data indicates no change or increased expression.

Example 5: Transformation of RNA Sequencing Data

The amount of RNA per immune cell type was determined.

RNA Per Cell Calculations

Immune cell types (CD4+ T cells, CD8+ T cells, B-cells, Monocytes, Treg and natural killer cells) were purified by flow cytometry from multiple peripheral blood mononuclear cell (PBMC) donors. Macrophages M1 and M2 were differentiated in cell culture from monocyte cell donors and purified using fluorescent activated cell sorting (FACs) to obtain pure M1 and M2 populations. RNA was extracted from the purified cells and sequenced. The number of cells obtained from FACS was recorded with the amount of RNA extracted from each cell enabling calculations for the amount of RNA per cell for each cell type. FIG. 9 shows the average amount of total RNA per cell for each immune cell type.

Cell Correction Methods

The effect on cell percentages and ratios calculated from deconvolution using SVM (support vector machines) when the different cell types contained distinct amounts of total RNA were determined. Cell mixtures were generated in duplicate from Macrophages M1 and M2 spiked into perinuclear blood mononuclear cell (PBMC) samples in decreasing ratios. These cell mixtures represent a “gold standard” or sample where the true answer (percentages of cell types in the mixture) was known before deconvolution. The cell mixture ratios are shown for PBMC samples comprising 500,000 cells in Table 7.

TABLE 7 Sample Name % Macrophage % PBMC M1-100 100 0 M1-50 50 50 M1-25 25 75 M1-10 10 90 M1-5 5 95 M1-2 2 98 M1-0 0 100 M2-100 100 0 M2-50 50 50 M2-25 25 75 M2-10 10 90 M2-5 5 95 M2-2 2 98 M2-0 0 100 *M1M2-100 100 0 M1M2-50 50 50 M1M2-25 25 75 M1M2-10 10 90 IvilM2-5 5 95 M1M2-2 2 98 M1M2-0 0 100 *M1M2 = 50% M1 + 50% M2 mix

Total RNA was extracted from the cell mixtures and sequenced. Following sequencing, the resulting data was analyzed for M1 and M2 cell percentages, using SVM-based deconvolution as described herein, and the computed cell type percentages were compared to the known percentages (ground truth). As seen in FIGS. 10A-10F, since the total RNA amount contained in macrophages is much higher than observed in other immune cells, the deconvolution method resulted in the calculation of a higher percentage of macrophage cells than as compared to truth. When observing FIG. 10A as a non-color drawing, at the leftmost data points on the chart, the M1 proportion data is shown in order from top to bottom in order as “expected”, “observed”, and “corrected”. In FIG. 10B, the highest M2 proportions are “observed” followed by “corrected” and then “expected”. In FIG. 10C, at the leftmost data points on the chart, the highest data point corresponds to expected followed by observed and then corrected. In FIG. 10D, the highest M2 proportions are “observed” followed by “corrected” and then “expected”. In FIG. 10E, at the leftmost data points on the chart, the highest data point corresponds to “expected” followed by “observed” and then “corrected”. In FIG. 10F, at the leftmost data points on the chart, the highest data point corresponds to “expected” followed by “observed” and then “corrected”. Based on these results, a method for correcting cell percentages for any cell type as required based on cellular RNA amount was developed. The equation below is one method for correcting cell percentages following deconvolution:

$\begin{matrix} {{{\left( {1 - o_{k}} \right)i_{k}m_{k}} - {\sum\limits_{j \neq k}{o_{k}m_{j}i_{j}}}} = 0} & {{Equation}\mspace{14mu} 1} \\ {{\sum i_{k}} = 1} & {{Equation}\mspace{14mu} 2} \end{matrix}$

Equation 1 was used for each of k cell types. Referring to the equation, o_(k) is the observed output i_(k) is the actuation output, and m_(k) is the multiplier. For each cell type equation, the sum subtracted is over the o, m, i values for the “other” cell types. All k equations of equation 1 were set to 1.The second equation is the constraint that all inputs add to 1.

Correction of Macrophages M1 and M2 Percentages

Because the amount of RNA in macrophage cells was much higher than that seen in other immune cell types, the analysis algorithms compute this increased amount of RNA as a greater percentage of cells than expected. In order to bring the percentage of macrophage cells in line with the expected percent, Equation 1 and Equation 2 were used. This correction translated the percentages from “transcript space” to “cell space” by applying a correction based on amount of RNA (transcripts) per cell. Once the equation is applied to the M1 and M2 cell percentage cells, the percentages highly resemble the expected percentages. The factor of correction used here was 12×. Results using methods as described herein are seen in Table 8.

TABLE 8 Cell correction value Amount of RNA per Cell for deconvolution Cell Type (pg/cell) (normalized to CD4+ T cell) CD4+ T cell 0.52 1.00 CD8+ T cell 0.54 1.03 Monocyte 0.71 1.35 B-cell 0.28 0.53 NK 0.24 0.47 M1 Macro 3.98 7.59 M2 Macro 6.44 12.26

Example 6—Cell Percentage Accuracy

The estimated cell percentages generated according to the methods disclosed herein were compared to known cell percentages calculated using flow cytometry to determine the accuracy of the deconvolution algorithm, as shown in FIG. 11. The percentage of immune cells in complex mixtures was measured using flow cytometry (y-axis=Known %) and compared to the estimated percentage of immune cell types from RNA sequencing data of the complex mixtures (x-axis=Estimated %). As shown in the graph, the cell percent estimates exhibit high trueness, precision, accuracy and correlation in comparison to the known percent.

This experiment estimating cell percentages and calculating true cell percentages using flow cytometry and was performed in triplicate, and one of the replicates was used to train for cell corrections in comparison to the known percent from flow. The data shown in FIG. 11 represents an assessment of the trained model using testing data (using the training corrections). Thus, this method corrected for deviations from the true cell percentages by training the model as opposed to using cell corrections based on RNA content/quantity per cell. The high accuracy of the model is indicated by the deviations indicated in FIG. 11, which are also shown in Table 9 below.

TABLE 9 estimated cell percentage deviation from true cell percentage % Deviation of Estimated Cell type/subtype Percentage from Known Percentage CD56 −0.01% +/− 0.94% Treg −0.23% +/− 0.61% CD4  0.77% +/− 1.52% CD14 −0.18% +/− 0.57% M1  0.21% +/− 0.16% M2  0.07% +/− 0.13% CD8 −0.03% +/− 0.73% CD19 −0.07% +/− 0.52%

Example 7—Clinical Sample Classification for Diagnosis and Prognosis

An immune-oncology profile that includes the relative quantities of 8 cell types and expression level for 10 immune-inhibitory genes (e.g., “escape genes”) was determined for 15-20 biological samples obtained from human subjects according to the methods described herein. The samples were previously categorized into two groups: subjects who were responsive to a stated therapy and subjects who were not responsive to the therapy.

The immune-oncology profile was used to understand differences across two groups of samples based on single or a combination of analytes used as predictive biomarker(s). Specifically, the immune-oncology profile analyte information was used to train a machine learning algorithm for classifying samples into the two groups.

The machine learning algorithm was used to generate classifiers based on individual analytes and multiple analytes. Single analyte biomarkers were used to solve for a threshold that maximizes the sensitivity and sensitivity simultaneously. With a large enough (normal) distribution of samples, this criteria may maximize the accuracy. Based on the small sample set (˜10 in each group), which is typical in many studies such as early phase clinical trials, this optimization metric best approximates where the maximal accuracy may be if more samples were available.

Multi analyte biomarkers were found by optimizing the same statistics. Instead of using a linear threshold for single analytes, a random forest model was optimized to maximize the above predictive statistics. The algorithms chose the random forest model with the best set of individual analytes and the best set of hyper-parameters (e.g., the tuning knobs of the random forest technique).

The predictive accuracies calculated for the most predictive escape gene (“escape”) and the most predictive immune cell type (“immune”). Also shown is the predictive accuracy of using one or more analytes in the Paragon Assay (“PARAGON”). This “marker” is created by learning a machine learning model that incorporates information from one or more analytes. These results are shown in the predictive accuracy bar plot in FIG. 12A. The “escape” biomarker and “immune” biomarker both generated a predictive accuracy of just under 75%. Meanwhile, the “paragon” multi-analyte classifier resulted in an 85% predictive accuracy, demonstrating how the multi-analyte approach produced superior accuracy in the context of small sample sizes.

FIG. 12B shows box-and-whisker plots that visualize the statistics for groups of samples for the 2 most predictive analytes. The left and right sides of the box indicate the 1st and 3rd quartiles of the respective data set. The median is indicated by the white line inside the box. The minimum and maximum inlier data points are denoted by the ends of the whiskers, while outliers are shown as empty circles. The optimal threshold for a given analyte is shown as a vertical dotted line. Wilcoxon rank-sum testing is used to test the null hypothesis that the two groups are sampled from the same distribution. Significance of rejecting this hypothesis is denoted for p-values of <0.05, <0.01, and <0.001 by 1, 2, and 3 stars, respectively.

In this case, the “escape” biomarker identified as being the most predictive of the list of 10 immune-inhibitory genes assessed by the algorithm was CTLA4, which produced the just below 75% predictive accuracy when used to group a sample based on a threshold CTLA4 expression level. As shown in FIG. 12B, the dotted line indicates a threshold value of about 5 TPM (transcripts per kilobase million) separating the two groups or categories of samples. Likewise, the cell type identified as the most predictive “immune” biomarker was CD19+ B cells. As shown in FIG. 12C, a threshold value just above 30% separates the two sample categories. A flow chart illustrating the generation of a single-analyte classifier and a multi-analyte classifier is shown in FIG. 13. In single-analyte/biomarker analysis, the individual analyte is assessed by determining the threshold that maximizes sensitivity and specificity (steps 1-4 in FIG. 13). Separate predictors or classifiers are generated for each analyte. In multi-analyte analysis, the most predictive analytes are combined to generate a combination predictor or classifier based on multiple analytes (e.g., multiple immune escape gene(s) and/or immune cell(s) percentages infiltrating the tumor sample) (steps 5-10).

The statistical performance of these models was tested using the leave-one-out cross validation to calculate the accuracy, positive predictive value (ppv), and negative predictive value (npv) for each analyte. For a dataset limited in size, leave-one-out cross validation gives the best approximation to how an estimator will generalize to future, independent samples. The process works by iterating n times (where there are n data points), each time learning a threshold considering n-1 points and testing the prediction of the nth, left out, point. Then, all n predictions were considered to calculate prediction statistics. Thresholds were determined by optimizing equally for sensitivity and specificity using all samples. For data points that are normally distributed, this threshold may be the same threshold optimized for accuracy. The results of the statistical assessment of the model and/or analyte performance are shown below in Table 10.

TABLE 10 DF1n DF3y accu- thresh- ppv Median Median npv racy old Analyte (%) (TPM) (TPM) (%) (%) (TPM) p-value CTLA4 71.42 0.97 20.59 66.66 69.23 4.78 0.0151 OX40 71.42 3.65 7.79 66.66 69.23 5.56 0.0864 PD-1 66.66 1.12 2.52 57.14 61.53 1.35 0.253 IDO1 57.14 7.22 3.13 50 53.84 5.46 0.475 CD47 57.14 71.77 51.14 50 53.84 65 0.475 PD-L1 57.14 3.64 3.89 50 53.84 3.77 0.475 TIM-3 57.14 15.8 13.83 50 53.84 13.71 0.5677 BTLA 57.14 0.29 0.28 50 53.84 0.33 0.775 ICOS 57.14 2.23 1.56 50 53.84 1.58 0.8303 ARG1 57.14 12.23 17.78 50 53.84 14.57 0.8864 M2 71.42 16.5 2 66.66 69.23 11.11 0.0455 Macro- phages CD19+ 71.42 14 54 66.66 69.23 32.39 0.0455 B Cells CD14+ 71.42 39.5 12 66.66 69.23 28.87 0.2246 Mono- cytes CD56+ 80 0 7 62.5 69.23 0 0.3531 NK Cells CD+ 100 0 0 54.54 61.53 0 0.3913 T Cells Treg 100 0 0 50 53.84 0 0.6682 Cells CD4+ 57.14 5.5 7 50 53.84 7.24 0.7209 T Cells M1 50 3.5 3 42.85 46.15 3.01 0.775 Macro- phages Paragon 100 N/A N/A 75 84.61 N/A N/A

While preferred embodiments of the present disclosure have been shown and described herein, it will be obvious to those skilled in the art that such embodiments are provided by way of example only. Numerous variations, changes, and substitutions will now occur to those skilled in the art without departing from the disclosure. It should be understood that various alternatives to the embodiments of the disclosure described herein may be employed in practicing the disclosure. It is intended that the following claims define the scope of the disclosure and that methods and structures within the scope of these claims and their equivalents be covered thereby. 

What is claimed is:
 1. A computer-implemented method for analyzing a biological sample obtained from a subject having or suspected of having a disease or condition, comprising: (a) obtaining gene expression data comprising (i) an expression level of at least one immune modulatory gene and (ii) expression levels of a plurality of expression signature genes from the biological sample; (b) using a deconvolution algorithm to process said expression levels of said plurality of expression signature genes to identify and quantify a percentage of at least one cell type that is present in the biological sample; and (c) using a classifier to analyze the expression level of the at least one immune modulatory gene and the percentage of the at least one cell type from (b) to determine a likelihood that said subject will be responsive or non-responsive to therapy.
 2. The method of claim 1, wherein the therapy comprises immunotherapy.
 3. The method of claim 1, further comprising providing instructions to start, stop, change, or continue the therapy.
 4. The method of claim 1, wherein the disease or condition is cancer, and wherein (c) comprises determining that said likelihood that said subject will be responsive or non-responsive to said therapy for said cancer.
 5. The method of claim 1, wherein the at least one cell type comprises at least one immune cell type.
 6. The method of claim 5, wherein the at least one immune cell type comprises M1 macrophages, M2 macrophages, CD19+ B cells, CD14+ monocytes, CD56+ NK cells, CD8+ T cells, Treg cells, CD4+ T cells, or any combination thereof.
 7. The method of claim 1, wherein the at least one immune modulatory gene comprises CTLA4, OX40, PD-1, IDO1, CD47, PD-L1, TIM-3, BTLA, ICOS, ARG1, or any combination thereof.
 8. The method of claim 1, wherein the classifier is generated using a machine learning algorithm.
 9. The method of claim 8, wherein the machine learning algorithm is a random forest algorithm.
 10. The method of claim 1, wherein the deconvolution algorithm in (b) applies a deconvolution matrix to process said expression levels of said plurality of expression signature genes to identify and quantify the percentage of the at least one cell type.
 11. The method of claim 10, wherein the deconvolution matrix comprises a plurality of immune cell expression signature genes.
 12. The method of claim 10, wherein the deconvolution matrix comprises a plurality of tumor cell expression signature genes.
 13. The method of claim 10, wherein the deconvolution matrix comprises a plurality of cell types, each cell type comprising a plurality of expression signature genes, wherein expression count for each expression signature gene is normalized across the plurality of cell types.
 14. The method of claim 1, wherein the deconvolution algorithm processes said expression levels of said plurality of expression signature genes using linear least-squares regression (LLSR), quadratic programming (QP), perturbation model for gene expression deconvolution (PERT), robust linear regression (RLR), microarray microdissection with analysis of differences (MMAD), digital sorting algorithm (DSA), or support vector regression.
 15. The method of claim 14, wherein the deconvolution algorithm performs an RNA normalization step to compensate for variation in RNA quantity amongst the at least one cell type in order to improve accuracy of the percentage of the at least one cell type.
 16. The method of claim 15, wherein the deconvolution algorithm is a machine learning algorithm trained using comparison data comprising an actual percentage of the at least one cell type.
 17. The method of claim 1, wherein the gene expression data and the plurality of expression signature genes are obtained from the biological sample using next generation RNA sequencing.
 18. The method of claim 1, further comprising processing the gene expression data to determine mutational burden for the biological sample and inputting the mutational burden into the classifier for analysis in order to enhance classification of the biological sample.
 19. The method of claim 1, wherein the classifier is trained on data from no more than 50 samples and provides an accuracy of at least 85%.
 20. A system comprising for analyzing a biological sample obtained from a subject having or suspected of having a disease or condition, comprising: a database comprising gene expression data comprising (i) an expression level of at least one immune modulatory gene and (ii) expression levels of a plurality of expression signature genes from the biological sample; and at least one computer processor that is coupled to said database, wherein said at least one computer processor is programmed to: (a) use a deconvolution algorithm to process said expression levels of said plurality of expression signature genes to identify and quantify a percentage of at least one cell type that is present in the biological sample; (b) use a classifier to analyze the expression level of the at least one immune modulatory gene and the percentage of the at least one cell type from (b) to determine a likelihood that said subject will be responsive or non-responsive to therapy.
 21. The system of claim 20, wherein the at least one cell type comprises M1 macrophages, M2 macrophages, CD19+ B cells, CD14+ monocytes, CD56+ NK cells, CD8+ T cells, Treg cells, CD4+ T cells, or any combination thereof.
 22. The system of claim 20, wherein the at least one immune modulatory gene comprises CTLA4, OX40, PD-1, IDO1, CD47, PD-L1, TIM-3, BTLA, ICOS, ARG1, or any combination thereof.
 23. The system of claim 20, wherein the classifier is generated using a machine learning algorithm.
 24. The system of claim 23, wherein the machine learning algorithm is a random forest algorithm.
 25. The system of claim 20, wherein the deconvolution algorithm in (a) applies a deconvolution matrix to process said expression levels of said plurality of expression signature genes to identify and quantify the percentage of the at least one cell type.
 26. The system of claim 25, wherein the deconvolution algorithm performs an RNA normalization step to compensate for variation in RNA quantity amongst the at least one cell type in order to improve accuracy of the percentage of the at least one cell type.
 27. The system of claim 20, wherein the gene expression data and the plurality of expression signature genes are obtained from the biological sample using next generation RNA sequencing.
 28. The system of claim 27, wherein the at least one processor is further programmed to obtain mutational burden data for the biological sample and inputting the mutational burden data into the classifier for analysis in order to enhance classification of the biological sample.
 29. The system of any one of claims 20, wherein the classifier is trained on data from no more than 50 samples and provides an accuracy of at least 85%.
 30. Non-transitory computer readable medium comprising machine executable code that, upon execution by one or more computer processors, performs a method comprising: (a) obtaining gene expression data comprising (i) an expression level of at least one immune modulatory gene and (ii) expression levels of a plurality of expression signature genes from the biological sample; (b) using a deconvolution algorithm to process said expression levels of said plurality of expression signature genes to identify and quantify a percentage of at least one cell type that is present in the biological sample; and (c) using a classifier to analyze the expression level of the at least one immune modulatory gene and the percentage of the at least one cell type from (b) to determine a likelihood that said subject will be responsive or non-responsive to therapy. 